DUF3302 - PFAM28P - GREMLIN Contacts

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DUF3302 - Protein of unknown function (DUF3302)

PFAM:	PF11742	Sequences: LDYFALVVLIVVPAVAIAVFVLLHILPGKIAKKRNHPQADAIHVLGWLSLFFGGVLWPLAWIWAYTDRPDRGWGFSQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	77 (65)
Sequences:	3339 (1193)
Seq/√Len:	147.9
META:	0.95

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
3_Y	7_V	3.406	1.00
45_L	60_A	3.132	1.00
32_K	43_H	2.249	1.00
42_I	66_T	1.953	1.00
15_V	19_V	1.723	1.00
28_G	39_A	1.668	1.00
7_V	11_V	1.549	1.00
4_F	8_V	1.546	1.00
34_R	40_D	1.478	1.00
21_V	25_I	1.461	1.00
32_K	39_A	1.405	1.00
46_G	49_S	1.374	1.00
4_F	7_V	1.373	1.00
36_H	63_W	1.366	1.00
52_F	55_V	1.324	1.00
28_G	46_G	1.305	1.00
40_D	43_H	1.304	1.00
30_I	34_R	1.281	1.00
55_V	58_P	1.278	1.00
48_L	61_W	1.238	1.00
6_L	10_I	1.196	1.00
26_L	30_I	1.181	1.00
24_H	47_W	1.180	1.00
57_W	61_W	1.172	1.00
18_A	22_L	1.152	1.00
44_V	61_W	1.148	1.00
30_I	65_Y	1.147	1.00
18_A	21_V	1.129	0.99
49_S	60_A	1.126	0.99
38_Q	66_T	1.121	0.99
38_Q	42_I	1.098	0.99
12_V	21_V	1.089	0.99
12_V	16_A	1.071	0.99
39_A	43_H	1.060	0.99
44_V	65_Y	1.046	0.99
45_L	59_L	1.045	0.99
17_I	21_V	1.039	0.99
24_H	46_G	1.037	0.99
8_V	12_V	1.032	0.99
48_L	57_W	1.007	0.99
25_I	29_K	0.997	0.99
6_L	9_L	0.991	0.99
11_V	15_V	0.982	0.99
20_F	24_H	0.980	0.99
22_L	26_L	0.972	0.98
41_A	63_W	0.963	0.98
49_S	58_P	0.963	0.98
50_L	53_G	0.949	0.98
51_F	65_Y	0.922	0.98
29_K	32_K	0.908	0.98
22_L	29_K	0.906	0.98
14_A	18_A	0.898	0.97
45_L	56_L	0.897	0.97
20_F	50_L	0.886	0.97
16_A	19_V	0.869	0.97
34_R	65_Y	0.863	0.97
50_L	57_W	0.845	0.96
30_I	33_K	0.844	0.96
24_H	50_L	0.841	0.96
9_L	13_P	0.822	0.96
19_V	22_L	0.801	0.95
56_L	59_L	0.789	0.94
28_G	32_K	0.779	0.94
23_L	26_L	0.767	0.94
35_N	39_A	0.764	0.93
45_L	58_P	0.744	0.93
32_K	35_N	0.738	0.92
19_V	23_L	0.730	0.92
4_F	11_V	0.729	0.92
6_L	52_F	0.726	0.92
43_H	47_W	0.710	0.91
49_S	54_G	0.695	0.90
38_Q	48_L	0.680	0.89
3_Y	6_L	0.675	0.88
20_F	46_G	0.658	0.87
41_A	50_L	0.654	0.87
25_I	46_G	0.651	0.87
29_K	33_K	0.643	0.86
27_P	31_A	0.640	0.86
2_D	6_L	0.639	0.86
39_A	46_G	0.625	0.84
19_V	56_L	0.623	0.84
47_W	51_F	0.598	0.82
26_L	65_Y	0.594	0.81
2_D	17_I	0.589	0.81
5_A	15_V	0.584	0.80
16_A	20_F	0.582	0.80
28_G	44_V	0.557	0.77
26_L	29_K	0.555	0.77
2_D	8_V	0.551	0.76
48_L	53_G	0.531	0.74
18_A	26_L	0.530	0.73
37_P	41_A	0.528	0.73
12_V	17_I	0.520	0.72
49_S	55_V	0.517	0.72
8_V	11_V	0.512	0.71
61_W	65_Y	0.504	0.70
33_K	66_T	0.500	0.69

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
2wswA	3	0.6104	5	0.91	Contact Map
4p02B	1	0.3636	3.1	0.919	Contact Map
4tllB	2	0.3636	2.6	0.922	Contact Map
1wazA	1	0.3506	1.9	0.927	Contact Map
4c7rA	3	0.961	1.9	0.928	Contact Map
4gb7A	1	0.3247	1.8	0.928	Contact Map
2mofA	1	0.5325	1.7	0.929	Contact Map
1pi7A	1	0.2468	1.6	0.93	Contact Map
3ne5A	3	0.8701	1.6	0.931	Contact Map
4ccfA	3	0	1.5	0.932	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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