DUF4806 - PFAM28P - GREMLIN Contacts

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DUF4806 - Domain of unknown function (DUF4806)

PFAM:	PF16064	Sequences: SVPGFDFPLKTEEDLEELEEKLKNDEEFRKKLVKYLSRIGGKKNSVRRILKKLFTDELASKYSWTGRKGKGKKAFKNLKIFCKVILEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	88 (77)
Sequences:	606 (563)
Seq/√Len:	64.1
META:	0.031

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
12_E	62_Y	3.128	1.00
12_E	73_K	2.787	1.00
29_R	33_V	2.637	1.00
56_D	59_A	2.495	1.00
75_F	78_L	2.397	1.00
21_K	28_F	2.270	1.00
11_T	14_D	2.262	1.00
54_F	59_A	2.226	1.00
10_K	55_T	2.122	1.00
62_Y	73_K	2.114	1.00
63_S	68_K	2.083	1.00
9_L	18_L	2.064	1.00
9_L	58_L	2.050	1.00
15_L	78_L	1.796	1.00
10_K	57_E	1.793	1.00
72_K	75_F	1.788	1.00
15_L	58_L	1.746	1.00
64_W	82_C	1.659	0.99
74_A	77_N	1.535	0.99
13_E	17_E	1.524	0.99
9_L	15_L	1.456	0.98
28_F	32_L	1.447	0.98
36_L	53_L	1.390	0.97
26_E	57_E	1.356	0.97
66_G	72_K	1.320	0.97
76_K	81_F	1.300	0.96
63_S	74_A	1.281	0.96
54_F	58_L	1.220	0.95
59_A	64_W	1.182	0.94
51_K	56_D	1.179	0.94
14_D	26_E	1.162	0.93
11_T	15_L	1.137	0.92
44_N	52_K	1.108	0.91
14_D	17_E	1.085	0.90
55_T	58_L	1.019	0.87
33_V	37_S	1.013	0.87
54_F	81_F	0.973	0.85
9_L	19_E	0.971	0.85
46_V	56_D	0.961	0.84
22_L	32_L	0.950	0.83
65_T	76_K	0.946	0.83
17_E	21_K	0.904	0.80
16_E	51_K	0.886	0.79
13_E	26_E	0.884	0.79
41_G	48_R	0.878	0.78
13_E	24_N	0.873	0.78
63_S	66_G	0.867	0.77
62_Y	78_L	0.850	0.76
16_E	78_L	0.850	0.76
27_E	32_L	0.845	0.76
55_T	67_R	0.822	0.74
7_F	69_G	0.818	0.73
65_T	69_G	0.800	0.72
18_L	22_L	0.793	0.71
45_S	50_L	0.790	0.71
17_E	25_D	0.773	0.69
25_D	64_W	0.767	0.68
22_L	61_K	0.766	0.68
7_F	46_V	0.760	0.68
49_I	63_S	0.744	0.66
36_L	74_A	0.740	0.66
44_N	48_R	0.717	0.63
26_E	74_A	0.710	0.62
34_K	60_S	0.706	0.62
64_W	67_R	0.680	0.59
63_S	69_G	0.674	0.58
22_L	52_K	0.672	0.58
18_L	25_D	0.661	0.57
11_T	18_L	0.658	0.56
20_E	24_N	0.654	0.56
45_S	49_I	0.652	0.56
47_R	63_S	0.649	0.55
16_E	25_D	0.648	0.55
62_Y	68_K	0.648	0.55
47_R	50_L	0.646	0.55
44_N	67_R	0.644	0.55
78_L	81_F	0.638	0.54
19_E	33_V	0.634	0.54
35_Y	62_Y	0.632	0.54
10_K	13_E	0.630	0.53
15_L	54_F	0.629	0.53
64_W	75_F	0.621	0.52
19_E	65_T	0.618	0.52
7_F	51_K	0.614	0.51
33_V	60_S	0.612	0.51
48_R	67_R	0.607	0.51
21_K	33_V	0.602	0.50
43_K	47_R	0.597	0.49
12_E	53_L	0.587	0.48
21_K	32_L	0.581	0.48
23_K	79_K	0.579	0.47
17_E	20_E	0.578	0.47
61_K	84_V	0.577	0.47
12_E	72_K	0.577	0.47
39_I	46_V	0.576	0.47
10_K	14_D	0.566	0.46
36_L	49_I	0.565	0.46
53_L	75_F	0.561	0.45
28_F	63_S	0.560	0.45
64_W	69_G	0.556	0.45
56_D	63_S	0.550	0.44
82_C	85_I	0.549	0.44
35_Y	79_K	0.539	0.43
77_N	84_V	0.534	0.42
24_N	63_S	0.527	0.41
14_D	51_K	0.526	0.41
39_I	48_R	0.523	0.41
44_N	83_K	0.522	0.41
29_R	54_F	0.518	0.40
22_L	58_L	0.517	0.40
15_L	68_K	0.514	0.40
33_V	38_R	0.507	0.39
46_V	49_I	0.507	0.39
12_E	61_K	0.505	0.39
47_R	51_K	0.504	0.39
21_K	58_L	0.500	0.38

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
2ux8A	4	0.4659	21.3	0.862	Contact Map
3wvzA	2	0.3409	13.5	0.874	Contact Map
1u7lA	1	0.9432	11.5	0.878	Contact Map
4ix7A	1	0.8182	8.7	0.884	Contact Map
2e3dA	3	0.4545	7.4	0.889	Contact Map
3sxxA	5	0.8636	7.2	0.889	Contact Map
2fclA	1	0.3864	7.1	0.889	Contact Map
3ja82	1	0.8977	6.7	0.89	Contact Map
3i5qB	4	0.8636	5.3	0.895	Contact Map
1twfA	1	0.9886	5.2	0.896	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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