DUF4316 - PFAM28P - GREMLIN Contacts

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DUF4316 - Domain of unknown function (DUF4316)

PFAM:	PF14195	Sequences: PENPLKNAEMSTEQNYNMIDGIINNGPKEPTVAELEAKAEKEEKPEKKPSVLEQLKAKKEEAAKKKKAKEKSQELER	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	77 (72)
Sequences:	646 (433)
Seq/√Len:	51.0
META:	0.913

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_M	16_Y	3.418	1.00
16_Y	19_I	2.865	1.00
6_K	10_M	2.502	1.00
50_S	55_L	2.490	1.00
2_E	6_K	2.236	1.00
10_M	19_I	2.037	1.00
3_N	23_I	2.019	1.00
69_K	72_S	2.018	1.00
7_N	11_S	1.879	0.99
69_K	73_Q	1.873	0.99
8_A	19_I	1.864	0.99
8_A	16_Y	1.853	0.99
60_E	63_A	1.673	0.98
14_Q	17_N	1.533	0.97
12_T	19_I	1.501	0.97
48_K	55_L	1.463	0.96
3_N	21_G	1.457	0.96
12_T	23_I	1.405	0.95
26_G	29_E	1.392	0.95
70_E	73_Q	1.318	0.93
40_E	43_E	1.309	0.93
48_K	51_V	1.305	0.93
61_E	67_K	1.293	0.93
68_A	71_K	1.242	0.91
7_N	10_M	1.238	0.91
2_E	18_M	1.214	0.90
68_A	72_S	1.213	0.90
56_K	59_K	1.176	0.89
51_V	56_K	1.133	0.87
32_V	39_A	1.086	0.84
12_T	15_N	1.068	0.83
3_N	6_K	1.052	0.82
4_P	23_I	1.038	0.82
58_K	62_A	1.028	0.81
33_A	36_E	1.018	0.80
45_P	48_K	1.007	0.80
58_K	61_E	0.994	0.79
31_T	39_A	0.982	0.78
12_T	18_M	0.978	0.77
34_E	39_A	0.978	0.77
30_P	38_K	0.953	0.76
30_P	35_L	0.948	0.75
63_A	66_K	0.945	0.75
6_K	12_T	0.941	0.75
27_P	30_P	0.913	0.72
68_A	73_Q	0.910	0.72
7_N	12_T	0.881	0.70
14_Q	24_N	0.876	0.69
12_T	16_Y	0.873	0.69
10_M	14_Q	0.867	0.68
8_A	11_S	0.843	0.66
49_P	52_L	0.838	0.66
67_K	70_E	0.834	0.65
10_M	18_M	0.824	0.65
34_E	37_A	0.805	0.63
2_E	7_N	0.805	0.63
67_K	73_Q	0.796	0.62
7_N	21_G	0.794	0.62
62_A	66_K	0.791	0.61
6_K	15_N	0.787	0.61
56_K	66_K	0.771	0.59
53_E	57_A	0.757	0.58
31_T	34_E	0.757	0.58
64_K	68_A	0.752	0.57
31_T	36_E	0.751	0.57
11_S	22_I	0.722	0.54
15_N	26_G	0.721	0.54
4_P	8_A	0.718	0.54
61_E	64_K	0.710	0.53
52_L	58_K	0.695	0.52
46_E	53_E	0.685	0.51
51_V	58_K	0.677	0.50
36_E	39_A	0.671	0.49
51_V	55_L	0.667	0.49
15_N	18_M	0.667	0.49
52_L	55_L	0.661	0.48
34_E	38_K	0.653	0.47
57_A	70_E	0.650	0.47
2_E	10_M	0.634	0.45
54_Q	57_A	0.620	0.44
40_E	46_E	0.617	0.44
39_A	42_E	0.614	0.43
59_K	63_A	0.611	0.43
6_K	21_G	0.609	0.43
52_L	59_K	0.608	0.43
28_K	34_E	0.597	0.42
10_M	15_N	0.594	0.41
2_E	15_N	0.591	0.41
6_K	16_Y	0.591	0.41
30_P	39_A	0.590	0.41
7_N	19_I	0.587	0.41
32_V	38_K	0.570	0.39
53_E	60_E	0.568	0.39
57_A	64_K	0.567	0.39
63_A	70_E	0.559	0.38
32_V	37_A	0.551	0.37
56_K	62_A	0.545	0.36
64_K	70_E	0.533	0.35
4_P	16_Y	0.533	0.35
35_L	39_A	0.531	0.35
40_E	47_K	0.530	0.35
35_L	38_K	0.525	0.35
33_A	38_K	0.523	0.34
62_A	65_K	0.521	0.34
53_E	73_Q	0.511	0.33
64_K	67_K	0.507	0.33
14_Q	28_K	0.506	0.33
43_E	72_S	0.500	0.32

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
3ja83	1	0	6.1	0.895	Contact Map
3t49A	1	0.3247	2.9	0.91	Contact Map
1ywfA	1	0.5325	2.7	0.912	Contact Map
2winM	1	0.3506	1.8	0.92	Contact Map
4cpcA	4	0.5974	1.3	0.927	Contact Map
2xkxA	2	0.7013	1.2	0.928	Contact Map
4yhuA	1	0	1.1	0.929	Contact Map
5a1uH	1	0.4675	1	0.931	Contact Map
1o7dB	1	0.2208	1	0.931	Contact Map
4fgvA	1	0.4286	1	0.931	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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