DUF3288 - PFAM28P - GREMLIN Contacts

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DUF3288 - Protein of unknown function (DUF3288)

PFAM:	PF11691	Sequences: DQTHPLYATDRDIVDSLLAEEPEDLDLVELARLIIRYQGFPGARDIQNDLEKILKFWGLTEEELFEKTRAIHANGDVYGSGFDTSEQDW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	89 (86)
Sequences:	642 (351)
Seq/√Len:	37.8
META:	0.794

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_I	51_E	4.251	1.00
7_Y	45_D	4.177	1.00
1_D	44_R	3.137	1.00
27_L	68_T	2.911	1.00
44_R	47_Q	2.486	1.00
65_F	68_T	2.133	0.99
31_A	68_T	2.063	0.99
15_D	18_L	2.022	0.99
25_L	29_E	1.990	0.99
80_S	83_D	1.940	0.98
60_T	63_E	1.927	0.98
40_F	43_A	1.893	0.98
79_G	84_T	1.677	0.96
16_S	26_D	1.620	0.95
80_S	85_S	1.502	0.93
79_G	83_D	1.424	0.90
78_Y	81_G	1.415	0.90
23_E	26_D	1.408	0.90
59_L	67_K	1.394	0.89
11_R	45_D	1.340	0.87
67_K	70_A	1.335	0.87
43_A	50_L	1.277	0.85
76_D	83_D	1.267	0.84
22_P	57_W	1.263	0.84
15_D	49_D	1.217	0.82
11_R	49_D	1.214	0.82
82_F	86_E	1.198	0.81
27_L	40_F	1.175	0.79
30_L	53_I	1.159	0.79
27_L	59_L	1.151	0.78
25_L	46_I	1.140	0.77
45_D	49_D	1.122	0.76
58_G	62_E	1.114	0.76
81_G	84_T	1.105	0.75
16_S	20_E	1.095	0.74
19_A	39_G	1.094	0.74
59_L	63_E	1.063	0.72
76_D	82_F	1.037	0.70
7_Y	39_G	1.032	0.70
76_D	84_T	1.032	0.70
29_E	72_H	1.013	0.68
71_I	80_S	1.003	0.68
68_T	71_I	0.991	0.67
8_A	28_V	0.976	0.66
54_L	63_E	0.919	0.61
80_S	84_T	0.918	0.61
10_D	37_Y	0.911	0.60
17_L	57_W	0.890	0.58
83_D	86_E	0.886	0.58
13_I	50_L	0.879	0.57
51_E	63_E	0.874	0.57
13_I	17_L	0.867	0.56
20_E	26_D	0.860	0.56
34_I	61_E	0.850	0.55
82_F	85_S	0.847	0.55
72_H	78_Y	0.842	0.54
27_L	41_P	0.841	0.54
3_T	50_L	0.838	0.54
61_E	65_F	0.836	0.54
76_D	79_G	0.835	0.53
77_V	83_D	0.809	0.51
75_G	82_F	0.800	0.50
30_L	60_T	0.797	0.50
70_A	73_A	0.794	0.50
7_Y	80_S	0.793	0.50
76_D	80_S	0.790	0.49
72_H	75_G	0.774	0.48
38_Q	65_F	0.769	0.48
79_G	82_F	0.768	0.48
48_N	52_K	0.763	0.47
60_T	74_N	0.760	0.47
78_Y	83_D	0.760	0.47
35_I	38_Q	0.759	0.47
38_Q	61_E	0.756	0.46
7_Y	15_D	0.755	0.46
18_L	53_I	0.754	0.46
52_K	56_F	0.751	0.46
17_L	22_P	0.731	0.44
58_G	86_E	0.723	0.44
42_G	47_Q	0.723	0.44
50_L	65_F	0.721	0.43
72_H	77_V	0.720	0.43
75_G	78_Y	0.718	0.43
76_D	81_G	0.716	0.43
6_L	9_T	0.714	0.43
39_G	47_Q	0.712	0.43
18_L	29_E	0.701	0.42
21_E	74_N	0.698	0.41
79_G	86_E	0.691	0.41
29_E	32_R	0.684	0.40
74_N	77_V	0.679	0.40
9_T	12_D	0.667	0.39
62_E	74_N	0.661	0.38
7_Y	49_D	0.652	0.37
34_I	65_F	0.652	0.37
25_L	30_L	0.651	0.37
14_V	50_L	0.648	0.37
30_L	54_L	0.647	0.37
35_I	65_F	0.643	0.37
30_L	65_F	0.642	0.37
29_E	43_A	0.638	0.36
2_Q	5_P	0.636	0.36
63_E	66_E	0.632	0.36
46_I	65_F	0.632	0.36
26_D	32_R	0.613	0.34
1_D	71_I	0.610	0.34
14_V	17_L	0.600	0.33
18_L	49_D	0.586	0.32
17_L	30_L	0.581	0.32
21_E	26_D	0.581	0.32
23_E	73_A	0.576	0.31
74_N	86_E	0.572	0.31
24_D	39_G	0.570	0.31
14_V	33_L	0.568	0.31
49_D	52_K	0.562	0.30
35_I	44_R	0.561	0.30
43_A	47_Q	0.554	0.30
55_K	85_S	0.550	0.29
50_L	69_R	0.545	0.29
54_L	68_T	0.544	0.29
16_S	19_A	0.540	0.29
68_T	72_H	0.536	0.28
46_I	61_E	0.528	0.28
24_D	41_P	0.521	0.27
13_I	16_S	0.517	0.27
6_L	80_S	0.514	0.27
14_V	49_D	0.506	0.26
77_V	85_S	0.505	0.26
12_D	85_S	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
1qsaA	1	0.9438	13.3	0.927	Contact Map
4ch7A	1	0.6629	12	0.928	Contact Map
1q2fA	1	0.3596	10	0.931	Contact Map
4g9qA	3	0.6292	8.7	0.932	Contact Map
4lwlA	1	0.8427	8.6	0.933	Contact Map
4g55A	1	0.4045	7.9	0.934	Contact Map
1yubA	1	0.4944	7.6	0.934	Contact Map
1f6vA	1	0.6404	7	0.935	Contact Map
1vt0M	4	0.8315	6.1	0.937	Contact Map
2ggtA	1	0.6517	6.1	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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