DUF2788 - PFAM28P - GREMLIN Contacts

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DUF2788 - Protein of unknown function (DUF2788)

PFAM:	PF10981	Sequences: GVGGLILYMLFIIWDLAKESKAGKFGTFVLFLVLGLGMLGFVAKGVIQWFM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	51 (50)
Sequences:	1226 (460)
Seq/√Len:	65.1
META:	0.816

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_D	19_E	4.134	1.00
13_I	30_L	3.508	1.00
14_W	18_K	2.394	1.00
17_A	27_T	2.198	1.00
45_G	48_Q	1.867	1.00
32_L	36_L	1.638	0.99
3_G	7_L	1.551	0.99
43_A	47_I	1.513	0.99
13_I	35_G	1.503	0.99
37_G	40_G	1.482	0.98
8_Y	11_F	1.390	0.98
15_D	18_K	1.388	0.98
40_G	47_I	1.384	0.98
25_F	29_V	1.362	0.97
8_Y	15_D	1.356	0.97
28_F	32_L	1.339	0.97
45_G	49_W	1.293	0.96
10_L	38_M	1.248	0.95
46_V	50_F	1.238	0.95
14_W	31_F	1.196	0.94
7_L	11_F	1.185	0.94
33_V	36_L	1.157	0.93
22_A	26_G	1.150	0.93
6_I	38_M	1.138	0.93
4_G	7_L	1.067	0.90
33_V	45_G	1.047	0.89
17_A	21_K	0.979	0.86
13_I	38_M	0.949	0.84
25_F	28_F	0.943	0.83
20_S	31_F	0.882	0.79
39_L	42_V	0.868	0.78
1_G	32_L	0.838	0.76
6_I	9_M	0.836	0.75
39_L	43_A	0.824	0.74
12_I	17_A	0.823	0.74
42_V	45_G	0.815	0.73
21_K	31_F	0.789	0.71
1_G	4_G	0.783	0.70
10_L	33_V	0.775	0.70
12_I	23_G	0.773	0.69
8_Y	19_E	0.753	0.67
2_V	41_F	0.749	0.67
41_F	45_G	0.736	0.66
36_L	39_L	0.728	0.65
22_A	27_T	0.728	0.65
35_G	38_M	0.721	0.64
16_L	23_G	0.715	0.63
35_G	39_L	0.693	0.61
24_K	28_F	0.652	0.56
10_L	35_G	0.651	0.56
42_V	50_F	0.645	0.56
12_I	27_T	0.643	0.55
12_I	16_L	0.642	0.55
32_L	46_V	0.634	0.54
23_G	30_L	0.617	0.52
29_V	32_L	0.612	0.52
5_L	9_M	0.609	0.51
17_A	20_S	0.599	0.50
12_I	30_L	0.593	0.50
24_K	34_L	0.588	0.49
18_K	33_V	0.585	0.49
6_I	40_G	0.573	0.47
14_W	27_T	0.570	0.47
4_G	17_A	0.568	0.47
12_I	31_F	0.557	0.45
29_V	46_V	0.553	0.45
37_G	47_I	0.549	0.44
9_M	40_G	0.535	0.43
20_S	25_F	0.534	0.43
2_V	5_L	0.525	0.42
17_A	23_G	0.518	0.41
1_G	5_L	0.511	0.40
2_V	36_L	0.508	0.40
2_V	28_F	0.503	0.39
32_L	39_L	0.500	0.39

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
2w1kA	1	0	7.6	0.87	Contact Map
1afoA	2	0.3725	4.2	0.885	Contact Map
4cbfA	7	0.7451	3.1	0.892	Contact Map
3j27A	7	0.7451	2.9	0.894	Contact Map
4cctA	7	0.7451	2.9	0.894	Contact Map
2k21A	1	1	2.8	0.895	Contact Map
2ph5A	2	0.549	2.7	0.895	Contact Map
4plpA	2	0.5686	1.6	0.907	Contact Map
3hunA	1	0	1.6	0.908	Contact Map
1wazA	1	0.451	1.6	0.908	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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