DUF768 - PFAM28P - GREMLIN Contacts

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DUF768 - Protein of unknown function (DUF768)

PFAM:	PF05589	Sequences: MSERALDFLEEWISENVPPTANADIARAKELAEQCLADAAAAGISAEEIEEEVGDLYEFILDAI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	64 (62)
Sequences:	865 (524)
Seq/√Len:	66.5
META:	0.892

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_K	33_E	2.443	1.00
9_L	53_V	2.111	1.00
19_P	22_N	2.102	1.00
44_I	48_E	2.090	1.00
3_E	7_D	2.032	1.00
15_E	33_E	1.980	1.00
46_A	50_E	1.952	1.00
50_E	54_G	1.873	1.00
9_L	48_E	1.752	1.00
4_R	48_E	1.742	1.00
16_N	34_Q	1.539	0.99
15_E	42_A	1.448	0.98
2_S	39_A	1.367	0.98
8_F	32_A	1.362	0.97
9_L	49_I	1.339	0.97
7_D	11_E	1.338	0.97
5_A	9_L	1.325	0.97
35_C	56_L	1.299	0.97
6_L	52_E	1.259	0.96
6_L	10_E	1.252	0.96
17_V	22_N	1.244	0.96
28_A	35_C	1.243	0.96
34_Q	37_A	1.241	0.96
5_A	8_F	1.180	0.94
28_A	60_I	1.178	0.94
17_V	20_T	1.163	0.94
34_Q	38_D	1.134	0.93
18_P	22_N	1.102	0.92
36_L	40_A	1.101	0.92
28_A	32_A	1.090	0.91
15_E	18_P	1.075	0.91
21_A	24_D	1.060	0.90
36_L	46_A	1.055	0.90
16_N	60_I	1.049	0.90
16_N	41_A	1.043	0.89
47_E	54_G	1.003	0.88
53_V	59_F	0.976	0.86
11_E	16_N	0.959	0.85
32_A	45_S	0.909	0.82
27_R	30_E	0.905	0.82
1_M	5_A	0.900	0.81
8_F	44_I	0.862	0.78
5_A	52_E	0.857	0.78
11_E	48_E	0.857	0.78
4_R	10_E	0.850	0.77
11_E	14_S	0.849	0.77
50_E	61_L	0.838	0.76
13_I	20_T	0.831	0.76
32_A	47_E	0.827	0.75
5_A	44_I	0.824	0.75
58_E	61_L	0.807	0.74
18_P	51_E	0.799	0.73
13_I	60_I	0.796	0.73
2_S	48_E	0.786	0.72
16_N	30_E	0.785	0.72
17_V	40_A	0.784	0.71
7_D	45_S	0.779	0.71
55_D	59_F	0.764	0.69
21_A	27_R	0.760	0.69
13_I	37_A	0.757	0.69
38_D	41_A	0.745	0.68
19_P	40_A	0.741	0.67
50_E	56_L	0.740	0.67
19_P	30_E	0.732	0.66
59_F	62_D	0.728	0.66
25_I	36_L	0.726	0.66
6_L	54_G	0.722	0.65
32_A	58_E	0.722	0.65
41_A	51_E	0.715	0.64
8_F	12_W	0.712	0.64
20_T	30_E	0.712	0.64
31_L	42_A	0.698	0.62
40_A	50_E	0.692	0.62
56_L	60_I	0.678	0.60
35_C	50_E	0.678	0.60
16_N	38_D	0.665	0.59
56_L	59_F	0.659	0.58
10_E	26_A	0.640	0.56
53_V	58_E	0.636	0.55
21_A	26_A	0.631	0.55
10_E	14_S	0.622	0.54
13_I	57_Y	0.607	0.52
48_E	51_E	0.601	0.51
45_S	52_E	0.596	0.51
25_I	42_A	0.577	0.48
39_A	54_G	0.576	0.48
28_A	57_Y	0.575	0.48
45_S	48_E	0.566	0.47
17_V	31_L	0.564	0.47
17_V	57_Y	0.549	0.45
26_A	34_Q	0.544	0.45
53_V	56_L	0.526	0.42
33_E	53_V	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
3g5sA	1	0.3125	21.4	0.85	Contact Map
4ok9A	5	1	17.5	0.856	Contact Map
4xpxA	1	0.4688	12.4	0.865	Contact Map
1wpuA	6	0.9375	11.2	0.868	Contact Map
2m9xA	1	1	10.1	0.871	Contact Map
4p72A	2	0.7812	9.5	0.872	Contact Map
1exeA	2	0.5625	9.4	0.872	Contact Map
1p71A	2	0.5625	8.8	0.874	Contact Map
4p3vA	2	0.5625	8.5	0.875	Contact Map
1mulA	2	0.5625	8.4	0.875	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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