DUF3085 - PFAM28P - GREMLIN Contacts

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DUF3085 - Protein of unknown function (DUF3085)

PFAM:	PF11284	Sequences: PGLWLVKDEGVYLMSNGGPKLPDGKRPLVAYAEGCNPDTDPDDWWERKRAAFGGDDFAEFIPLEVLERLLAAAGGTDLRISLTETSISLQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	90 (87)
Sequences:	755 (539)
Seq/√Len:	57.8
META:	0.764

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
2_G	60_F	3.622	1.00
52_F	57_F	3.210	1.00
7_K	57_F	2.982	1.00
7_K	48_K	2.821	1.00
7_K	52_F	2.690	1.00
36_N	39_T	2.647	1.00
48_K	57_F	2.545	1.00
34_G	40_D	2.227	1.00
49_R	53_G	1.947	1.00
34_G	57_F	1.922	1.00
9_E	44_W	1.885	1.00
4_W	58_A	1.870	1.00
46_E	49_R	1.841	1.00
9_E	38_D	1.790	0.99
11_V	35_C	1.769	0.99
40_D	47_R	1.646	0.99
67_E	71_A	1.639	0.99
1_P	16_N	1.596	0.99
82_L	87_I	1.588	0.99
48_K	52_F	1.500	0.98
4_W	16_N	1.466	0.97
45_W	49_R	1.457	0.97
35_C	52_F	1.418	0.97
16_N	60_F	1.411	0.97
35_C	47_R	1.397	0.97
11_V	52_F	1.321	0.95
35_C	51_A	1.314	0.95
35_C	44_W	1.254	0.94
13_L	78_L	1.231	0.93
8_D	12_Y	1.183	0.92
11_V	51_A	1.175	0.91
2_G	16_N	1.092	0.88
50_A	53_G	1.071	0.87
48_K	53_G	1.071	0.87
7_K	11_V	1.058	0.87
6_V	29_V	1.057	0.86
23_D	27_P	1.036	0.85
6_V	14_M	1.022	0.85
7_K	51_A	1.021	0.85
11_V	32_A	1.013	0.84
34_G	47_R	1.009	0.84
44_W	48_K	1.007	0.84
13_L	44_W	1.003	0.83
16_N	19_P	0.980	0.82
65_V	69_L	0.977	0.82
50_A	54_G	0.973	0.82
62_P	65_V	0.938	0.79
33_E	77_D	0.924	0.78
81_S	88_S	0.912	0.77
15_S	19_P	0.900	0.76
51_A	82_L	0.900	0.76
44_W	47_R	0.878	0.74
14_M	32_A	0.870	0.74
51_A	57_F	0.870	0.74
80_I	87_I	0.859	0.73
47_R	51_A	0.853	0.72
68_R	71_A	0.842	0.71
83_T	86_S	0.841	0.71
1_P	17_G	0.823	0.70
46_E	50_A	0.822	0.69
49_R	54_G	0.818	0.69
49_R	55_D	0.804	0.68
32_A	52_F	0.795	0.67
71_A	84_E	0.784	0.66
7_K	47_R	0.778	0.65
34_G	58_A	0.776	0.65
6_V	32_A	0.750	0.62
55_D	58_A	0.746	0.62
12_Y	56_D	0.743	0.62
21_L	64_E	0.741	0.61
85_T	88_S	0.738	0.61
3_L	15_S	0.735	0.61
45_W	56_D	0.735	0.61
31_Y	37_P	0.727	0.60
7_K	35_C	0.718	0.59
63_L	67_E	0.712	0.58
33_E	41_P	0.712	0.58
44_W	53_G	0.711	0.58
62_P	78_L	0.702	0.57
13_L	32_A	0.702	0.57
65_V	68_R	0.689	0.56
43_D	46_E	0.676	0.54
61_I	84_E	0.674	0.54
83_T	88_S	0.660	0.53
9_E	51_A	0.658	0.52
33_E	36_N	0.657	0.52
69_L	80_I	0.654	0.52
26_R	79_R	0.652	0.52
1_P	19_P	0.651	0.52
31_Y	55_D	0.643	0.51
1_P	18_G	0.640	0.50
24_G	27_P	0.639	0.50
30_A	70_L	0.634	0.50
11_V	15_S	0.626	0.49
4_W	45_W	0.620	0.48
36_N	40_D	0.618	0.48
29_V	55_D	0.616	0.48
35_C	53_G	0.608	0.47
79_R	89_L	0.607	0.47
20_K	23_D	0.601	0.46
52_F	59_E	0.596	0.46
51_A	87_I	0.595	0.45
6_V	75_G	0.589	0.45
68_R	80_I	0.582	0.44
38_D	44_W	0.580	0.44
20_K	66_L	0.571	0.43
55_D	61_I	0.566	0.42
5_L	24_G	0.564	0.42
10_G	34_G	0.557	0.41
20_K	39_T	0.556	0.41
40_D	43_D	0.550	0.41
65_V	78_L	0.549	0.41
30_A	40_D	0.548	0.40
52_F	82_L	0.540	0.40
66_L	81_S	0.539	0.39
44_W	51_A	0.539	0.39
61_I	73_A	0.537	0.39
56_D	83_T	0.536	0.39
36_N	44_W	0.534	0.39
66_L	74_G	0.532	0.39
23_D	26_R	0.525	0.38
55_D	59_E	0.521	0.38
34_G	52_F	0.520	0.37
37_P	73_A	0.512	0.37
8_D	56_D	0.511	0.37
36_N	69_L	0.504	0.36
24_G	70_L	0.504	0.36
21_L	27_P	0.503	0.36
35_C	57_F	0.501	0.36
5_L	52_F	0.500	0.35

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
3c0uA	2	0.9667	24.7	0.901	Contact Map
2g3wA	2	0.9667	22.6	0.903	Contact Map
2ot9A	1	0.9444	19.3	0.906	Contact Map
4o4oA	2	0.6333	16.5	0.909	Contact Map
3s9jA	1	0.3889	9.4	0.918	Contact Map
3oakC	1	0.3333	6.1	0.925	Contact Map
2rh0A	2	0.5667	5.4	0.927	Contact Map
4epuA	2	0.9	5.3	0.927	Contact Map
2mxyA	1	0.8	4.4	0.929	Contact Map
2xsdC	1	0.3333	4.2	0.93	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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