DUF2758 - PFAM28P - GREMLIN Contacts

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DUF2758 - Protein of unknown function (DUF2758)

PFAM:	PF10957	Sequences: MMKVKIFDEEHEKDLEEAINEFLEELDEIEIIDIKYQVAISIEFGEEQIYCFSAMIIYKA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	60 (58)
Sequences:	586 (450)
Seq/√Len:	59.1
META:	0.775

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_L	29_I	3.346	1.00
35_K	57_I	2.476	1.00
7_F	56_I	2.435	1.00
5_K	16_E	2.278	1.00
17_E	21_E	2.094	1.00
36_Y	53_S	2.093	1.00
30_E	59_K	1.888	1.00
23_L	29_I	1.708	0.99
24_E	29_I	1.643	0.99
42_I	45_G	1.616	0.99
21_E	27_D	1.576	0.99
13_K	16_E	1.575	0.99
22_F	58_Y	1.549	0.98
44_F	47_E	1.523	0.98
6_I	13_K	1.428	0.97
47_E	52_F	1.411	0.97
41_S	44_F	1.388	0.97
18_A	21_E	1.326	0.96
26_L	31_I	1.310	0.95
6_I	37_Q	1.245	0.94
48_Q	51_C	1.241	0.94
28_E	59_K	1.239	0.94
21_E	25_E	1.213	0.93
43_E	46_E	1.209	0.93
34_I	54_A	1.206	0.93
24_E	28_E	1.203	0.93
9_E	18_A	1.166	0.92
8_D	48_Q	1.163	0.92
19_I	56_I	1.153	0.91
40_I	51_C	1.098	0.89
27_D	59_K	1.051	0.87
4_V	22_F	1.034	0.86
9_E	15_L	1.019	0.85
4_V	19_I	0.995	0.84
17_E	30_E	0.977	0.83
8_D	14_D	0.938	0.80
11_H	14_D	0.933	0.80
8_D	12_E	0.870	0.75
7_F	19_I	0.867	0.74
11_H	50_Y	0.844	0.72
39_A	50_Y	0.796	0.68
29_I	36_Y	0.781	0.66
16_E	58_Y	0.765	0.65
12_E	48_Q	0.753	0.64
6_I	56_I	0.750	0.63
12_E	53_S	0.742	0.62
2_M	58_Y	0.739	0.62
14_D	52_F	0.731	0.61
12_E	50_Y	0.727	0.61
17_E	56_I	0.712	0.59
4_V	23_L	0.708	0.59
32_I	57_I	0.706	0.59
41_S	53_S	0.687	0.57
54_A	58_Y	0.677	0.55
15_L	52_F	0.674	0.55
8_D	49_I	0.667	0.54
7_F	36_Y	0.665	0.54
11_H	39_A	0.652	0.53
31_I	44_F	0.644	0.52
35_K	38_V	0.639	0.51
14_D	22_F	0.635	0.51
27_D	32_I	0.635	0.51
19_I	32_I	0.630	0.50
42_I	46_E	0.627	0.50
40_I	43_E	0.626	0.50
3_K	23_L	0.625	0.50
52_F	55_M	0.620	0.49
30_E	33_D	0.617	0.49
19_I	31_I	0.614	0.48
12_E	15_L	0.613	0.48
6_I	59_K	0.603	0.47
26_L	30_E	0.573	0.44
12_E	49_I	0.566	0.43
19_I	54_A	0.564	0.43
7_F	44_F	0.562	0.43
14_D	51_C	0.555	0.42
29_I	32_I	0.553	0.42
21_E	46_E	0.550	0.41
10_E	17_E	0.549	0.41
37_Q	55_M	0.534	0.40
40_I	50_Y	0.532	0.39
44_F	56_I	0.531	0.39
19_I	26_L	0.529	0.39
2_M	45_G	0.509	0.37
25_E	56_I	0.506	0.37
48_Q	52_F	0.504	0.36
12_E	52_F	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
2iayA	1	0.5833	7.6	0.872	Contact Map
3j80C	1	0.9333	7.5	0.872	Contact Map
3bgyA	1	0.75	6.9	0.874	Contact Map
4bpeE	1	0.9333	6.2	0.877	Contact Map
4ujpD	1	0.95	6.2	0.877	Contact Map
4kzyC	1	0.9333	6.1	0.878	Contact Map
3j60C	1	0.9333	6	0.878	Contact Map
5a2qC	1	0.9333	5.8	0.879	Contact Map
3zeyP	1	0.9333	5.2	0.881	Contact Map
3j7aG	1	0.9333	4.2	0.886	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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