DUF2388 - PFAM28P - GREMLIN Contacts

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DUF2388 - Protein of unknown function (DUF2388)

PFAM:	PF09498	Sequences: VASSGDATSSTTSSSRDDKLVLAARDDAASFVASDGAIRGARLEAALRHLRQQNPQLQASDLELAQAILA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	70 (69)
Sequences:	878 (394)
Seq/√Len:	47.4
META:	0.517

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_F	39_R	3.181	1.00
39_R	44_E	3.092	1.00
30_S	38_I	2.960	1.00
2_A	6_D	2.437	1.00
9_S	12_T	2.358	1.00
29_A	69_L	2.018	0.99
34_S	38_I	1.958	0.99
6_D	10_S	1.901	0.99
11_T	15_S	1.875	0.99
3_S	7_A	1.769	0.99
6_D	9_S	1.745	0.98
3_S	11_T	1.678	0.98
12_T	15_S	1.672	0.98
3_S	6_D	1.595	0.97
5_G	10_S	1.587	0.97
2_A	5_G	1.526	0.96
24_A	46_A	1.482	0.96
7_A	11_T	1.313	0.92
41_A	48_R	1.283	0.91
61_D	64_L	1.230	0.89
39_R	61_D	1.227	0.89
43_L	50_L	1.221	0.89
26_D	40_G	1.192	0.87
3_S	10_S	1.166	0.86
5_G	8_T	1.140	0.85
32_V	67_A	1.124	0.84
12_T	16_R	1.082	0.82
7_A	10_S	1.070	0.81
32_V	43_L	1.063	0.81
47_L	62_L	1.014	0.77
35_D	66_Q	1.003	0.77
50_L	55_P	0.996	0.76
6_D	11_T	0.978	0.75
23_A	42_R	0.977	0.75
18_D	49_H	0.971	0.74
11_T	16_R	0.957	0.73
45_A	69_L	0.945	0.72
6_D	16_R	0.943	0.72
64_L	67_A	0.936	0.71
28_A	43_L	0.933	0.71
4_S	13_S	0.925	0.71
8_T	16_R	0.923	0.70
28_A	40_G	0.899	0.68
54_N	57_L	0.888	0.67
39_R	59_A	0.875	0.66
30_S	37_A	0.872	0.66
5_G	58_Q	0.860	0.65
12_T	29_A	0.850	0.64
7_A	12_T	0.845	0.63
60_S	63_E	0.844	0.63
46_A	68_I	0.840	0.63
47_L	61_D	0.840	0.63
44_E	48_R	0.837	0.63
48_R	52_Q	0.832	0.62
6_D	15_S	0.824	0.62
51_R	68_I	0.821	0.61
4_S	70_A	0.820	0.61
43_L	47_L	0.819	0.61
26_D	62_L	0.784	0.58
59_A	63_E	0.775	0.57
43_L	59_A	0.771	0.56
24_A	29_A	0.767	0.56
4_S	33_A	0.756	0.55
28_A	50_L	0.739	0.53
26_D	67_A	0.725	0.52
8_T	20_L	0.704	0.50
41_A	66_Q	0.702	0.50
19_K	50_L	0.695	0.49
60_S	66_Q	0.694	0.49
14_S	54_N	0.688	0.48
7_A	15_S	0.687	0.48
29_A	50_L	0.687	0.48
37_A	59_A	0.686	0.48
49_H	53_Q	0.675	0.47
51_R	64_L	0.672	0.47
42_R	48_R	0.670	0.46
32_V	68_I	0.668	0.46
51_R	61_D	0.657	0.45
15_S	70_A	0.653	0.45
23_A	32_V	0.637	0.43
41_A	62_L	0.635	0.43
13_S	49_H	0.626	0.42
25_R	46_A	0.612	0.41
49_H	63_E	0.610	0.40
4_S	27_D	0.609	0.40
29_A	45_A	0.606	0.40
5_G	11_T	0.599	0.39
2_A	48_R	0.594	0.39
40_G	44_E	0.585	0.38
2_A	7_A	0.581	0.38
22_L	53_Q	0.574	0.37
47_L	51_R	0.566	0.36
46_A	70_A	0.548	0.35
19_K	69_L	0.546	0.35
4_S	9_S	0.538	0.34
65_A	68_I	0.538	0.34
8_T	17_D	0.533	0.33
35_D	56_Q	0.531	0.33
20_L	49_H	0.527	0.33
30_S	40_G	0.520	0.32
14_S	18_D	0.508	0.31
11_T	14_S	0.507	0.31
62_L	66_Q	0.501	0.31
8_T	13_S	0.500	0.30

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
1vq0A	2	0.6714	22	0.87	Contact Map
1vzyA	3	0.6571	18.8	0.873	Contact Map
1i7fA	2	0.6571	18.3	0.874	Contact Map
1hw7A	2	0.6571	16.2	0.877	Contact Map
3iwfA	2	0.4	6.5	0.898	Contact Map
2o3fA	1	0.3857	5.9	0.899	Contact Map
4ivnA	2	0.3714	3.6	0.909	Contact Map
2m6yA	1	0.8571	2.8	0.914	Contact Map
1wwpA	2	0.4143	2.8	0.914	Contact Map
3vu1A	2	0.3857	2.8	0.914	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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