DUF2835 - PFAM28P - GREMLIN Contacts

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DUF2835 - Protein of unknown function (DUF2835)

PFAM:	PF11197	Sequences: YRFSLNISAEEYLRYYQGAARSVVVRARDGRRVQFPASHLRPFVTHDGIHGRFRLTFDDNNKFVSLER	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	68 (67)
Sequences:	1660 (1254)
Seq/√Len:	153.2
META:	0.804

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_R	52_R	2.959	1.00
6_N	50_H	2.552	1.00
54_R	67_E	2.448	1.00
4_S	28_R	2.290	1.00
24_V	32_R	2.220	1.00
39_H	63_F	2.171	1.00
22_S	34_Q	2.104	1.00
3_F	25_V	2.056	1.00
24_V	34_Q	1.970	1.00
35_F	40_L	1.932	1.00
27_A	31_R	1.903	1.00
12_Y	44_V	1.865	1.00
26_R	32_R	1.707	1.00
47_D	50_H	1.617	1.00
11_E	14_R	1.587	1.00
13_L	17_Q	1.520	1.00
2_R	54_R	1.503	1.00
4_S	52_R	1.445	1.00
56_T	67_E	1.415	1.00
15_Y	37_A	1.407	1.00
56_T	65_S	1.379	1.00
38_S	41_R	1.333	1.00
12_Y	37_A	1.332	1.00
23_V	40_L	1.284	1.00
14_R	19_A	1.214	1.00
57_F	61_N	1.195	1.00
3_F	66_L	1.184	1.00
8_S	11_E	1.165	1.00
2_R	28_R	1.146	1.00
58_D	64_V	1.118	1.00
63_F	66_L	1.101	0.99
35_F	55_L	1.083	0.99
7_I	12_Y	1.077	0.99
5_L	40_L	0.992	0.99
58_D	62_K	0.986	0.99
30_G	40_L	0.978	0.99
43_F	66_L	0.941	0.98
55_L	66_L	0.938	0.98
22_S	35_F	0.920	0.98
2_R	52_R	0.909	0.98
9_A	13_L	0.909	0.98
57_F	63_F	0.898	0.98
39_H	66_L	0.850	0.97
36_P	62_K	0.846	0.97
36_P	39_H	0.841	0.96
39_H	55_L	0.824	0.96
9_A	12_Y	0.819	0.96
36_P	57_F	0.793	0.95
26_R	42_P	0.783	0.95
39_H	43_F	0.777	0.95
37_A	41_R	0.770	0.94
20_A	32_R	0.763	0.94
3_F	15_Y	0.756	0.94
5_L	35_F	0.751	0.94
14_R	17_Q	0.750	0.93
25_V	35_F	0.736	0.93
39_H	57_F	0.732	0.93
12_Y	40_L	0.726	0.92
21_R	38_S	0.708	0.91
12_Y	49_I	0.704	0.91
9_A	44_V	0.684	0.90
41_R	44_V	0.675	0.89
10_E	13_L	0.671	0.89
29_D	57_F	0.667	0.89
6_N	47_D	0.659	0.88
17_Q	41_R	0.657	0.88
9_A	46_H	0.654	0.88
31_R	46_H	0.634	0.86
56_T	64_V	0.629	0.86
40_L	55_L	0.628	0.86
14_R	20_A	0.626	0.85
18_G	41_R	0.626	0.85
35_F	49_I	0.616	0.85
18_G	37_A	0.608	0.84
38_S	62_K	0.605	0.83
23_V	49_I	0.599	0.83
30_G	42_P	0.594	0.82
15_Y	43_F	0.590	0.82
23_V	37_A	0.589	0.82
7_I	11_E	0.583	0.81
25_V	28_R	0.577	0.81
14_R	27_A	0.575	0.80
58_D	61_N	0.571	0.80
36_P	63_F	0.571	0.80
39_H	62_K	0.558	0.78
7_I	21_R	0.556	0.78
18_G	21_R	0.549	0.77
57_F	62_K	0.540	0.76
23_V	35_F	0.535	0.75
4_S	46_H	0.530	0.75
15_Y	44_V	0.530	0.75
45_T	56_T	0.526	0.74
13_L	41_R	0.525	0.74
34_Q	62_K	0.523	0.74
26_R	67_E	0.519	0.73
20_A	37_A	0.516	0.73
31_R	57_F	0.514	0.72
43_F	53_F	0.507	0.71
21_R	41_R	0.503	0.71
17_Q	44_V	0.500	0.70

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
2do3A	1	0.5735	36.4	0.864	Contact Map
1wp5A	1	0.9706	26.4	0.874	Contact Map
3l6vA	1	0.9706	25.1	0.875	Contact Map
1zi0A	1	0.9559	23.2	0.877	Contact Map
1zvtA	1	0.9412	19.7	0.881	Contact Map
4g3nA	1	0.9706	17.6	0.884	Contact Map
1suuA	1	0.9559	15.4	0.886	Contact Map
3no0A	1	0.9559	13.1	0.89	Contact Map
1zvuA	2	0.9559	12.7	0.89	Contact Map
4lx3A	1	0.8382	11.6	0.892	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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