DUF2439 - PFAM28P - GREMLIN Contacts

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DUF2439 - Protein of unknown function (DUF2439)

PFAM:	PF10382	Sequences: VKEFRVLYTHQKTKKAKKWQDGFLKLHTFNKRVMLYDEDGNLLGSRFLKNKDEELQEGEELELDRYLVEVGEPVGTTETDI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	81 (75)
Sequences:	558 (431)
Seq/√Len:	49.8
META:	0.323

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_K	18_K	4.398	1.00
60_E	69_E	3.489	1.00
12_K	62_E	3.447	1.00
9_T	67_L	2.683	1.00
6_V	35_L	2.624	1.00
11_Q	14_K	2.594	1.00
23_F	40_G	2.153	1.00
35_L	66_Y	2.106	1.00
63_L	68_V	2.036	1.00
11_Q	18_K	1.973	0.99
14_K	67_L	1.734	0.99
18_K	32_R	1.724	0.99
3_E	25_K	1.564	0.97
10_H	69_E	1.534	0.97
34_M	42_L	1.494	0.96
8_Y	39_D	1.471	0.96
2_K	76_T	1.435	0.96
32_R	45_S	1.415	0.95
24_L	58_G	1.410	0.95
9_T	20_Q	1.385	0.95
5_R	74_V	1.357	0.94
55_L	59_E	1.353	0.94
29_F	34_M	1.329	0.93
43_L	66_Y	1.314	0.93
12_K	67_L	1.298	0.92
4_F	19_W	1.268	0.91
37_D	41_N	1.242	0.91
44_G	47_F	1.226	0.90
27_H	32_R	1.172	0.88
6_V	47_F	1.118	0.85
14_K	69_E	1.099	0.84
2_K	73_P	1.033	0.80
28_T	34_M	0.970	0.76
58_G	69_E	0.966	0.76
36_Y	48_L	0.962	0.75
2_K	12_K	0.956	0.75
43_L	46_R	0.953	0.75
4_F	71_G	0.949	0.74
27_H	30_N	0.928	0.73
25_K	29_F	0.915	0.72
23_F	59_E	0.909	0.71
36_Y	42_L	0.887	0.69
32_R	54_E	0.876	0.68
56_Q	59_E	0.869	0.68
9_T	12_K	0.858	0.67
12_K	19_W	0.845	0.65
10_H	40_G	0.807	0.62
55_L	70_V	0.800	0.61
37_D	48_L	0.786	0.60
25_K	54_E	0.779	0.59
37_D	68_V	0.776	0.59
14_K	64_D	0.755	0.57
55_L	61_L	0.753	0.57
57_E	72_E	0.750	0.56
21_D	34_M	0.747	0.56
39_D	42_L	0.734	0.55
73_P	76_T	0.729	0.54
33_V	63_L	0.727	0.54
23_F	64_D	0.719	0.53
21_D	32_R	0.718	0.53
73_P	77_T	0.717	0.53
30_N	47_F	0.714	0.53
4_F	58_G	0.709	0.52
65_R	70_V	0.709	0.52
4_F	7_L	0.703	0.51
38_E	72_E	0.688	0.50
65_R	73_P	0.684	0.50
31_K	38_E	0.677	0.49
46_R	63_L	0.669	0.48
4_F	33_V	0.667	0.48
7_L	69_E	0.663	0.47
29_F	32_R	0.661	0.47
57_E	75_G	0.653	0.46
9_T	16_A	0.640	0.45
30_N	45_S	0.640	0.45
23_F	55_L	0.631	0.44
46_R	53_E	0.630	0.44
22_G	35_L	0.627	0.44
55_L	58_G	0.623	0.43
5_R	32_R	0.623	0.43
7_L	10_H	0.620	0.43
2_K	26_L	0.618	0.43
20_Q	53_E	0.612	0.42
7_L	29_F	0.611	0.42
24_L	53_E	0.605	0.42
14_K	42_L	0.602	0.41
8_Y	20_Q	0.602	0.41
38_E	64_D	0.601	0.41
37_D	46_R	0.592	0.40
12_K	71_G	0.587	0.40
61_L	70_V	0.571	0.38
49_K	59_E	0.566	0.38
30_N	63_L	0.565	0.38
19_W	57_E	0.565	0.38
15_K	68_V	0.562	0.37
6_V	34_M	0.559	0.37
3_E	29_F	0.556	0.37
8_Y	77_T	0.552	0.36
35_L	44_G	0.544	0.36
41_N	74_V	0.533	0.35
41_N	45_S	0.529	0.34
28_T	32_R	0.526	0.34
3_E	69_E	0.522	0.34
7_L	61_L	0.521	0.34
5_R	72_E	0.520	0.33
2_K	8_Y	0.513	0.33
15_K	26_L	0.506	0.32
3_E	40_G	0.504	0.32
25_K	70_V	0.503	0.32
42_L	70_V	0.503	0.32
24_L	33_V	0.502	0.32
48_L	55_L	0.500	0.32

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
2b5uA	1	0.8272	26.6	0.863	Contact Map
4by2A	1	0.1111	10.7	0.886	Contact Map
4ld1A	1	0.358	8.3	0.891	Contact Map
4nooA	1	0.5556	6.6	0.897	Contact Map
1e6yB	2	0.5185	5.6	0.9	Contact Map
3sqgB	2	0.5062	5	0.902	Contact Map
1hbnB	2	0.5556	4.4	0.905	Contact Map
3u2gA	2	0.9877	3.4	0.909	Contact Map
3ecqA	1	0.8765	2.9	0.913	Contact Map
2bbrA	1	0.321	2.5	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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