DUF2929 - PFAM28P - GREMLIN Contacts

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DUF2929 - Protein of unknown function (DUF2929)

PFAM:	PF11151	Sequences: MRYIVTFFWSFLLGQMLGYVVSSLTGGTFDFTTGAILSVVFTVLVFIIGAIIPNES	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	56 (55)
Sequences:	547 (439)
Seq/√Len:	59.2
META:	0.314

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_G	34_G	3.307	1.00
13_L	16_M	2.972	1.00
15_Q	29_F	2.596	1.00
4_I	8_F	2.256	1.00
29_F	35_A	1.865	1.00
11_F	35_A	1.848	1.00
42_T	46_F	1.809	0.99
7_F	38_S	1.794	0.99
12_L	16_M	1.714	0.99
1_M	13_L	1.617	0.99
5_V	8_F	1.606	0.99
46_F	50_A	1.601	0.99
17_L	21_V	1.580	0.99
19_Y	24_L	1.476	0.98
15_Q	35_A	1.466	0.98
26_G	37_L	1.453	0.98
15_Q	24_L	1.397	0.97
30_D	33_T	1.360	0.96
11_F	36_I	1.316	0.96
14_G	38_S	1.303	0.95
11_F	39_V	1.247	0.94
18_G	24_L	1.216	0.93
23_S	26_G	1.063	0.87
6_T	10_S	1.058	0.87
14_G	41_F	1.055	0.87
3_Y	32_T	1.003	0.84
16_M	20_V	0.995	0.84
44_L	48_I	0.956	0.81
15_Q	31_F	0.954	0.81
19_Y	49_G	0.948	0.81
5_V	24_L	0.927	0.79
10_S	38_S	0.917	0.78
39_V	42_T	0.895	0.77
33_T	36_I	0.892	0.76
10_S	21_V	0.853	0.73
49_G	52_I	0.851	0.73
19_Y	23_S	0.838	0.72
35_A	38_S	0.827	0.71
21_V	25_T	0.810	0.69
2_R	24_L	0.810	0.69
2_R	7_F	0.808	0.69
7_F	47_I	0.801	0.68
7_F	42_T	0.788	0.67
3_Y	6_T	0.764	0.65
43_V	50_A	0.763	0.65
48_I	51_I	0.755	0.64
50_A	53_P	0.742	0.62
1_M	23_S	0.740	0.62
20_V	52_I	0.738	0.62
32_T	40_V	0.736	0.62
38_S	54_N	0.723	0.60
5_V	37_L	0.722	0.60
35_A	47_I	0.711	0.59
20_V	41_F	0.688	0.57
44_L	52_I	0.662	0.54
16_M	24_L	0.657	0.53
34_G	38_S	0.654	0.53
43_V	51_I	0.638	0.51
47_I	52_I	0.631	0.50
10_S	40_V	0.626	0.50
26_G	33_T	0.622	0.49
36_I	41_F	0.621	0.49
14_G	42_T	0.608	0.48
7_F	39_V	0.603	0.47
2_R	18_G	0.588	0.46
19_Y	27_G	0.576	0.44
47_I	51_I	0.575	0.44
18_G	21_V	0.569	0.43
5_V	12_L	0.563	0.43
18_G	29_F	0.561	0.43
10_S	36_I	0.550	0.41
22_S	31_F	0.549	0.41
45_V	53_P	0.548	0.41
41_F	44_L	0.548	0.41
32_T	36_I	0.542	0.41
21_V	42_T	0.524	0.39
4_I	39_V	0.521	0.38
27_G	39_V	0.513	0.37
37_L	40_V	0.512	0.37
16_M	22_S	0.510	0.37
21_V	41_F	0.503	0.36
22_S	27_G	0.500	0.36

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
4pypA	1	1	8	0.852	Contact Map
3wdoA	1	1	7.6	0.853	Contact Map
1pw4A	1	1	6.3	0.859	Contact Map
4ldsA	2	1	6.1	0.859	Contact Map
2gfpA	2	1	5.3	0.863	Contact Map
4j05A	3	0.875	4.6	0.867	Contact Map
4gc0A	1	1	4.4	0.868	Contact Map
3iyzA	3	0.9821	4	0.871	Contact Map
4w251	1	0.7679	3.8	0.873	Contact Map
2zz9A	3	0.9821	3.5	0.874	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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