DUF2823 - PFAM28P - GREMLIN Contacts

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DUF2823 - Protein of unknown function (DUF2823)

PFAM:	PF11034	Sequences: MDTIKNAANYVSEKVQEATSGASKEANKEVAKDSNASLGTRASAAKDAVGDKVDEKKHEAKAEAHKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	67 (67)
Sequences:	775 (482)
Seq/√Len:	58.9
META:	0.796

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
23_S	51_D	2.707	1.00
24_K	48_A	2.653	1.00
63_E	67_E	2.612	1.00
23_S	27_N	2.175	1.00
4_I	8_A	1.891	1.00
17_E	59_E	1.828	1.00
13_E	61_K	1.796	0.99
56_K	59_E	1.790	0.99
20_S	54_D	1.788	0.99
16_Q	58_H	1.773	0.99
38_L	42_A	1.743	0.99
42_A	46_K	1.717	0.99
61_K	65_H	1.710	0.99
30_V	36_A	1.626	0.99
13_E	58_H	1.600	0.99
21_G	55_E	1.398	0.97
2_D	6_N	1.390	0.97
20_S	58_H	1.382	0.97
20_S	51_D	1.354	0.96
18_A	21_G	1.327	0.96
13_E	65_H	1.299	0.95
10_Y	62_A	1.236	0.94
63_E	66_K	1.215	0.93
55_E	59_E	1.192	0.92
14_K	18_A	1.173	0.92
46_K	49_V	1.166	0.92
12_S	16_Q	1.153	0.91
14_K	17_E	1.136	0.90
27_N	47_D	1.136	0.90
50_G	53_V	1.132	0.90
15_V	18_A	1.077	0.88
24_K	56_K	1.076	0.88
29_E	32_K	1.043	0.86
17_E	21_G	1.025	0.85
36_A	44_A	1.014	0.85
43_S	46_K	0.999	0.84
24_K	55_E	0.983	0.83
1_M	5_K	0.982	0.83
49_V	53_V	0.977	0.82
10_Y	14_K	0.947	0.80
9_N	12_S	0.913	0.78
31_A	41_R	0.902	0.77
3_T	6_N	0.902	0.77
30_V	44_A	0.892	0.76
17_E	55_E	0.888	0.76
36_A	40_T	0.888	0.76
40_T	43_S	0.886	0.76
37_S	40_T	0.872	0.75
21_G	24_K	0.872	0.75
7_A	11_V	0.851	0.73
42_A	45_A	0.838	0.72
46_K	50_G	0.837	0.72
2_D	33_D	0.826	0.71
45_A	50_G	0.818	0.70
54_D	57_K	0.806	0.69
25_E	35_N	0.805	0.69
53_V	57_K	0.764	0.65
27_N	51_D	0.759	0.64
6_N	65_H	0.758	0.64
60_A	63_E	0.757	0.64
45_A	49_V	0.731	0.61
53_V	56_K	0.731	0.61
7_A	10_Y	0.730	0.61
21_G	56_K	0.726	0.61
2_D	5_K	0.723	0.60
31_A	48_A	0.718	0.60
50_G	57_K	0.717	0.60
24_K	28_K	0.704	0.58
8_A	11_V	0.700	0.58
27_N	30_V	0.698	0.58
57_K	61_K	0.697	0.57
13_E	20_S	0.694	0.57
40_T	44_A	0.663	0.54
59_E	67_E	0.662	0.54
35_N	40_T	0.658	0.53
56_K	60_A	0.656	0.53
10_Y	18_A	0.650	0.52
60_A	64_A	0.646	0.52
30_V	40_T	0.634	0.50
33_D	36_A	0.626	0.50
13_E	16_Q	0.625	0.49
27_N	44_A	0.617	0.49
44_A	47_D	0.610	0.48
47_D	67_E	0.600	0.47
40_T	47_D	0.592	0.46
38_L	46_K	0.592	0.46
11_V	22_A	0.589	0.45
5_K	8_A	0.580	0.44
23_S	32_K	0.563	0.43
51_D	54_D	0.560	0.42
43_S	47_D	0.553	0.42
27_N	31_A	0.541	0.40
25_E	28_K	0.532	0.39
23_S	26_A	0.532	0.39
2_D	38_L	0.529	0.39
17_E	62_A	0.517	0.38
47_D	50_G	0.517	0.38
22_A	26_A	0.514	0.37
30_V	33_D	0.513	0.37
6_N	9_N	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
1iojA	1	0.7164	5.7	0.889	Contact Map
2l9qA	1	0.5224	3.6	0.9	Contact Map
2kfeA	1	0.2687	3.6	0.9	Contact Map
1pehA	1	0.3433	2.9	0.904	Contact Map
1l8wA	2	0.6866	2.6	0.907	Contact Map
2yk0A	1	0.4328	2.1	0.911	Contact Map
4po2A	4	0.6716	1.8	0.914	Contact Map
2wqdA	2	1	1.7	0.915	Contact Map
4f01A	2	0.6418	1.7	0.916	Contact Map
2nnuA	1	0.4478	1.7	0.916	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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