DUF504 - PFAM28P - GREMLIN Contacts

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DUF504 - Protein of unknown function (DUF504)

PFAM:	PF04457	Sequences: IGYYDRGAPGDIKRVPGSEIVFLEGSFFVEEGEEHSIPYHRIREIYYDGEVIWER	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	55 (55)
Sequences:	2254 (1724)
Seq/√Len:	232.5
META:	0.928

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_E	54_E	3.716	1.00
5_D	13_K	2.272	1.00
2_G	14_R	2.240	1.00
12_I	43_R	2.152	1.00
2_G	12_I	2.063	1.00
16_P	19_E	1.959	1.00
2_G	44_E	1.932	1.00
4_Y	43_R	1.920	1.00
31_E	34_E	1.884	1.00
46_Y	51_V	1.868	1.00
4_Y	9_P	1.745	1.00
8_A	11_D	1.677	1.00
7_G	11_D	1.639	1.00
5_D	8_A	1.501	1.00
29_V	36_S	1.392	1.00
14_R	46_Y	1.392	1.00
24_E	29_V	1.373	1.00
3_Y	24_E	1.245	1.00
29_V	34_E	1.177	1.00
51_V	54_E	1.166	1.00
27_F	36_S	1.127	1.00
1_I	20_I	1.113	1.00
22_F	29_V	1.082	1.00
4_Y	7_G	1.078	1.00
8_A	13_K	1.048	1.00
47_Y	50_E	1.040	1.00
4_Y	11_D	1.023	1.00
30_E	33_E	1.016	1.00
44_E	51_V	0.990	1.00
15_V	28_F	0.972	1.00
47_Y	55_R	0.960	1.00
21_V	34_E	0.959	1.00
32_G	35_H	0.930	1.00
2_G	46_Y	0.927	1.00
19_E	30_E	0.924	1.00
24_E	36_S	0.913	1.00
20_I	28_F	0.876	0.99
21_V	33_E	0.828	0.99
2_G	43_R	0.803	0.99
1_I	18_S	0.799	0.99
17_G	47_Y	0.795	0.99
17_G	45_I	0.789	0.99
23_L	26_S	0.779	0.99
23_L	28_F	0.771	0.98
17_G	25_G	0.765	0.98
5_D	11_D	0.762	0.98
7_G	10_G	0.758	0.98
5_D	26_S	0.731	0.98
2_G	53_W	0.692	0.97
30_E	34_E	0.686	0.97
23_L	39_Y	0.673	0.96
27_F	39_Y	0.666	0.96
18_S	47_Y	0.661	0.96
15_V	32_G	0.659	0.96
1_I	4_Y	0.656	0.96
14_R	22_F	0.651	0.96
18_S	25_G	0.640	0.95
5_D	53_W	0.629	0.95
28_F	36_S	0.623	0.94
24_E	27_F	0.622	0.94
40_H	53_W	0.622	0.94
13_K	17_G	0.613	0.94
23_L	42_I	0.611	0.94
46_Y	52_I	0.610	0.94
30_E	45_I	0.600	0.93
52_I	55_R	0.597	0.93
20_I	49_G	0.578	0.92
10_G	55_R	0.578	0.92
28_F	42_I	0.575	0.92
30_E	37_I	0.568	0.91
25_G	55_R	0.554	0.90
4_Y	35_H	0.543	0.89
3_Y	47_Y	0.541	0.89
28_F	39_Y	0.537	0.89
35_H	55_R	0.534	0.88
43_R	52_I	0.532	0.88
23_L	27_F	0.526	0.88
6_R	55_R	0.520	0.87
37_I	44_E	0.513	0.86
10_G	39_Y	0.511	0.86
22_F	39_Y	0.508	0.86
21_V	32_G	0.500	0.85

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
4c9sA	5	0.9091	22.3	0.803	Contact Map
3dc8A	3	0.9636	12.6	0.824	Contact Map
3sfwA	3	0.9636	10.4	0.83	Contact Map
4lcqA	3	0.9636	8.2	0.838	Contact Map
1nfgA	3	0.9636	8.1	0.838	Contact Map
3griA	1	0.9636	7.6	0.841	Contact Map
3g5kA	3	0.4	7.2	0.842	Contact Map
3hm7A	2	0.9636	6.8	0.844	Contact Map
2gwnA	1	0.9636	6	0.847	Contact Map
1gkpA	4	0.9636	6	0.847	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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