DUF2862 - PFAM28P - GREMLIN Contacts

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DUF2862 - Protein of unknown function (DUF2862)

PFAM:	PF11061	Sequences: IGQKVKLERVRDRLPKELIDALGKSPVGTISDFKMTDGKGIGVVVELSDGSETWFFEDEIE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	61 (60)
Sequences:	772 (377)
Seq/√Len:	48.6
META:	0.829

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_T	40_G	3.560	1.00
35_M	39_K	3.204	1.00
21_A	49_D	2.564	1.00
31_S	46_E	2.469	1.00
35_M	41_I	2.160	1.00
4_K	29_T	1.917	0.99
2_G	6_K	1.813	0.99
10_V	14_L	1.809	0.99
9_R	58_D	1.624	0.98
28_G	53_T	1.487	0.96
54_W	59_E	1.415	0.95
36_T	41_I	1.372	0.94
37_D	42_G	1.290	0.92
29_T	46_E	1.288	0.92
5_V	30_I	1.269	0.91
14_L	18_L	1.267	0.91
31_S	45_V	1.267	0.91
12_D	33_F	1.243	0.90
28_G	45_V	1.230	0.90
17_E	26_P	1.152	0.86
20_D	23_G	1.093	0.83
22_L	28_G	1.089	0.83
46_E	50_G	1.075	0.82
22_L	26_P	1.073	0.82
44_V	52_E	1.048	0.81
7_L	45_V	1.042	0.80
17_E	21_A	1.041	0.80
20_D	44_V	1.019	0.79
56_F	59_E	1.013	0.78
25_S	48_S	1.012	0.78
2_G	5_V	1.005	0.78
10_V	15_P	0.995	0.77
21_A	51_S	0.971	0.75
30_I	40_G	0.958	0.74
30_I	41_I	0.948	0.73
33_F	43_V	0.947	0.73
5_V	21_A	0.946	0.73
30_I	36_T	0.937	0.73
20_D	43_V	0.923	0.71
35_M	53_T	0.921	0.71
38_G	42_G	0.916	0.71
21_A	45_V	0.912	0.70
20_D	24_K	0.902	0.70
32_D	36_T	0.861	0.66
23_G	47_L	0.835	0.64
48_S	51_S	0.830	0.63
5_V	9_R	0.825	0.63
8_E	16_K	0.824	0.63
3_Q	6_K	0.824	0.63
43_V	57_E	0.821	0.62
23_G	26_P	0.813	0.62
6_K	15_P	0.807	0.61
15_P	22_L	0.805	0.61
10_V	18_L	0.800	0.60
1_I	6_K	0.761	0.56
43_V	50_G	0.759	0.56
6_K	44_V	0.752	0.56
16_K	20_D	0.750	0.55
36_T	51_S	0.748	0.55
19_I	45_V	0.727	0.53
3_Q	36_T	0.719	0.52
15_P	23_G	0.711	0.51
24_K	58_D	0.708	0.51
21_A	48_S	0.693	0.50
36_T	43_V	0.685	0.49
35_M	42_G	0.673	0.48
43_V	60_I	0.665	0.47
1_I	8_E	0.654	0.46
7_L	11_R	0.643	0.45
13_R	22_L	0.642	0.44
24_K	51_S	0.638	0.44
1_I	24_K	0.634	0.44
19_I	29_T	0.621	0.42
19_I	60_I	0.618	0.42
36_T	60_I	0.618	0.42
9_R	22_L	0.611	0.41
45_V	48_S	0.606	0.41
11_R	53_T	0.593	0.40
45_V	53_T	0.586	0.39
12_D	42_G	0.579	0.38
4_K	16_K	0.577	0.38
6_K	19_I	0.570	0.37
12_D	47_L	0.567	0.37
9_R	33_F	0.562	0.37
14_L	57_E	0.528	0.34
14_L	19_I	0.524	0.33
37_D	55_F	0.523	0.33
19_I	24_K	0.519	0.33
49_D	53_T	0.507	0.32
20_D	49_D	0.500	0.31

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
3ju0A	1	0.7213	45.9	0.856	Contact Map
4tseA	2	0.8852	45.8	0.856	Contact Map
3jtzA	2	0.7213	39.5	0.862	Contact Map
3db7A	2	0.9672	15.8	0.886	Contact Map
4qoaA	2	0.9508	12.8	0.89	Contact Map
4qqbX	1	0.623	12.2	0.892	Contact Map
4dsdA	1	0.9344	10.8	0.894	Contact Map
3lxrF	1	0.3934	10.8	0.894	Contact Map
4k61A	1	0.7869	10.3	0.895	Contact Map
1fx7A	4	0.9672	9.5	0.897	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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