DUF594 - PFAM28P - GREMLIN Contacts

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DUF594 - Protein of unknown function, DUF594

PFAM:	PF04578	Sequences: IEDEEKRWEVLADVWVEMLCYAAPSCRAEAHAKQLSRGGELITHVWLLLAHAGI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	54 (52)
Sequences:	1419 (777)
Seq/√Len:	107.7
META:	0.127

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_V	18_M	2.267	1.00
34_Q	37_R	2.171	1.00
14_V	17_E	2.086	1.00
10_V	17_E	2.035	1.00
17_E	20_C	1.882	1.00
26_C	32_A	1.807	1.00
24_P	27_R	1.673	1.00
46_W	54_I	1.649	1.00
8_W	44_H	1.572	1.00
3_D	6_K	1.472	1.00
14_V	52_A	1.440	1.00
27_R	30_A	1.317	0.99
22_A	42_I	1.304	0.99
30_A	44_H	1.283	0.99
23_A	42_I	1.241	0.99
7_R	52_A	1.237	0.99
30_A	36_S	1.235	0.99
10_V	14_V	1.212	0.99
35_L	41_L	1.184	0.99
23_A	50_A	1.175	0.99
4_E	9_E	1.166	0.99
42_I	45_V	1.147	0.98
16_V	32_A	1.147	0.98
9_E	13_D	1.140	0.98
14_V	20_C	1.131	0.98
7_R	11_L	1.125	0.98
16_V	20_C	1.120	0.98
29_E	33_K	1.062	0.97
9_E	12_A	1.060	0.97
28_A	42_I	1.029	0.97
18_M	22_A	1.028	0.97
12_A	16_V	1.024	0.97
41_L	50_A	1.004	0.96
21_Y	37_R	0.974	0.96
19_L	42_I	0.951	0.95
27_R	46_W	0.933	0.95
44_H	49_L	0.931	0.95
16_V	33_K	0.912	0.94
28_A	54_I	0.909	0.94
8_W	53_G	0.873	0.92
14_V	21_Y	0.871	0.92
10_V	36_S	0.857	0.92
20_C	29_E	0.854	0.92
13_D	16_V	0.846	0.91
39_G	44_H	0.836	0.91
10_V	13_D	0.834	0.91
7_R	35_L	0.819	0.90
34_Q	50_A	0.810	0.89
34_Q	44_H	0.793	0.88
4_E	40_E	0.791	0.88
29_E	34_Q	0.772	0.87
47_L	50_A	0.748	0.85
46_W	49_L	0.729	0.84
26_C	33_K	0.728	0.84
18_M	21_Y	0.719	0.83
8_W	48_L	0.711	0.82
26_C	50_A	0.707	0.82
12_A	49_L	0.698	0.81
6_K	33_K	0.696	0.81
47_L	51_H	0.694	0.81
19_L	45_V	0.692	0.80
7_R	10_V	0.687	0.80
20_C	49_L	0.656	0.77
27_R	34_Q	0.642	0.75
18_M	26_C	0.637	0.75
10_V	48_L	0.611	0.72
11_L	51_H	0.606	0.71
24_P	54_I	0.595	0.70
6_K	10_V	0.595	0.70
9_E	54_I	0.591	0.69
5_E	9_E	0.584	0.68
5_E	19_L	0.550	0.64
28_A	47_L	0.546	0.63
18_M	32_A	0.544	0.63
27_R	54_I	0.529	0.61
17_E	25_S	0.517	0.59
11_L	30_A	0.500	0.56
28_A	36_S	0.500	0.56

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
4okzA	1	1	4.7	0.895	Contact Map
3v1vA	2	1	4.4	0.896	Contact Map
4zq8A	2	1	3.7	0.9	Contact Map
1seiA	2	0.7963	3.6	0.901	Contact Map
1di1A	1	0.9444	3.6	0.901	Contact Map
3rf2A	1	0.7963	3.4	0.902	Contact Map
4pdbA	1	0.7963	3.4	0.902	Contact Map
4rb5H	1	0.7963	3.3	0.902	Contact Map
1s03H	1	0.7963	3	0.905	Contact Map
1i6uA	1	0.7963	2.9	0.905	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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