DUF3017 - PFAM28P - GREMLIN Contacts

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DUF3017 - Protein of unknown function (DUF3017)

PFAM:	PF11222	Sequences: YLLVLAGVAVGLVLVALGHWRRGTLVIGAALLLAAVLRLVLPERRAGLLAVRSRAVDVVTLAVLGAALLVLALT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	74 (72)
Sequences:	2858 (1779)
Seq/√Len:	209.6
META:	0.79

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_L	65_G	4.230	1.00
7_G	30_A	4.137	1.00
35_A	62_A	3.537	1.00
28_G	69_L	2.851	1.00
19_H	22_R	2.391	1.00
39_L	58_V	1.888	1.00
11_G	27_I	1.861	1.00
14_L	22_R	1.750	1.00
24_T	72_A	1.703	1.00
56_V	60_T	1.671	1.00
35_A	58_V	1.652	1.00
14_L	26_V	1.584	1.00
25_L	73_L	1.569	1.00
59_V	63_V	1.555	1.00
24_T	48_L	1.529	1.00
66_A	70_V	1.506	1.00
8_V	27_I	1.449	1.00
60_T	64_L	1.334	1.00
15_V	23_G	1.318	1.00
7_G	33_L	1.308	1.00
42_P	45_R	1.261	1.00
46_A	50_A	1.220	1.00
34_A	61_L	1.209	1.00
9_A	13_V	1.205	1.00
10_V	14_L	1.193	1.00
63_V	66_A	1.191	1.00
11_G	30_A	1.189	1.00
5_L	9_A	1.185	1.00
4_V	34_A	1.141	1.00
37_L	41_L	1.140	1.00
22_R	26_V	1.090	1.00
3_L	7_G	1.085	1.00
34_A	50_A	1.034	1.00
63_V	67_A	1.025	1.00
14_L	18_G	1.017	1.00
58_V	62_A	1.003	1.00
43_E	50_A	1.001	1.00
2_L	6_A	0.988	1.00
35_A	61_L	0.984	1.00
61_L	68_L	0.983	1.00
28_G	65_G	0.970	1.00
33_L	37_L	0.953	1.00
53_S	56_V	0.945	0.99
43_E	55_A	0.912	0.99
19_H	25_L	0.904	0.99
51_V	61_L	0.903	0.99
6_A	10_V	0.896	0.99
13_V	17_L	0.894	0.99
7_G	31_L	0.886	0.99
31_L	35_A	0.873	0.99
56_V	59_V	0.851	0.99
8_V	12_L	0.799	0.98
60_T	63_V	0.784	0.98
20_W	24_T	0.779	0.98
34_A	46_A	0.779	0.98
34_A	49_L	0.759	0.98
44_R	53_S	0.743	0.97
30_A	34_A	0.729	0.97
26_V	64_L	0.717	0.97
65_G	69_L	0.716	0.96
25_L	29_A	0.712	0.96
22_R	25_L	0.707	0.96
25_L	72_A	0.703	0.96
10_V	13_V	0.699	0.96
2_L	18_G	0.698	0.96
20_W	28_G	0.694	0.96
36_V	40_V	0.687	0.96
47_G	50_A	0.663	0.95
15_V	24_T	0.657	0.94
67_A	70_V	0.653	0.94
20_W	25_L	0.643	0.94
41_L	46_A	0.636	0.93
42_P	46_A	0.635	0.93
42_P	55_A	0.623	0.93
11_G	23_G	0.612	0.92
15_V	20_W	0.599	0.91
11_G	34_A	0.594	0.91
32_L	62_A	0.590	0.91
20_W	60_T	0.590	0.91
24_T	69_L	0.589	0.90
15_V	18_G	0.589	0.90
11_G	47_G	0.585	0.90
61_L	71_L	0.585	0.90
21_R	25_L	0.584	0.90
14_L	19_H	0.583	0.90
35_A	65_G	0.572	0.89
5_L	8_V	0.568	0.89
21_R	24_T	0.568	0.89
31_L	61_L	0.566	0.89
62_A	66_A	0.558	0.88
32_L	69_L	0.551	0.87
46_A	54_R	0.549	0.87
30_A	51_V	0.540	0.86
29_A	33_L	0.538	0.86
53_S	58_V	0.536	0.86
8_V	23_G	0.536	0.86
25_L	67_A	0.535	0.86
45_R	53_S	0.533	0.86
12_L	17_L	0.530	0.85
64_L	73_L	0.528	0.85
33_L	42_P	0.526	0.85
18_G	61_L	0.524	0.85
22_R	27_I	0.523	0.84
16_A	19_H	0.522	0.84
6_A	36_V	0.519	0.84
20_W	51_V	0.508	0.83
31_L	47_G	0.501	0.82
29_A	36_V	0.500	0.82

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
3hb3B	1	0	1.3	0.903	Contact Map
4i0uA	4	0.6081	1	0.91	Contact Map
4ev6A	3	0.6351	0.9	0.912	Contact Map
4phzB	3	0.4595	0.7	0.916	Contact Map
4pypA	1	0.9865	0.7	0.917	Contact Map
4pj0Y	1	0.3378	0.7	0.917	Contact Map
1orsC	1	0.3514	0.7	0.918	Contact Map
3wu2Y	1	0.3378	0.7	0.919	Contact Map
4bbjA	1	0.9459	0.6	0.92	Contact Map
4j05A	3	0.7838	0.6	0.92	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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