DUF3079 - PFAM28P - GREMLIN Contacts

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DUF3079 - Protein of unknown function (DUF3079)

PFAM:	PF11278	Sequences: MAKKFPLHPKHPERICWGCDKYCPADDLACGNGSIRTQHPVELFGDDWLEW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	51 (50)
Sequences:	1031 (335)
Seq/√Len:	47.4
META:	0.886

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_K	29_A	4.825	1.00
35_I	38_Q	3.913	1.00
11_H	14_R	3.069	1.00
28_L	37_T	2.506	1.00
8_H	46_D	1.681	0.98
5_F	34_S	1.489	0.96
33_G	37_T	1.465	0.95
36_R	41_V	1.395	0.94
35_I	44_F	1.385	0.94
8_H	41_V	1.373	0.93
16_C	19_C	1.365	0.93
3_K	37_T	1.364	0.93
22_Y	37_T	1.319	0.92
44_F	51_W	1.311	0.92
35_I	43_L	1.293	0.91
33_G	38_Q	1.197	0.88
45_G	48_W	1.175	0.87
36_R	49_L	1.156	0.86
3_K	6_P	1.121	0.84
8_H	38_Q	1.090	0.82
18_G	36_R	1.058	0.80
24_P	29_A	1.044	0.79
41_V	47_D	1.016	0.77
34_S	43_L	1.004	0.77
14_R	17_W	0.990	0.76
7_L	20_D	0.981	0.75
24_P	43_L	0.973	0.74
10_K	35_I	0.923	0.70
18_G	39_H	0.910	0.69
41_V	46_D	0.909	0.69
20_D	41_V	0.901	0.68
10_K	28_L	0.890	0.68
15_I	26_D	0.873	0.66
7_L	26_D	0.866	0.65
44_F	49_L	0.843	0.63
15_I	25_A	0.834	0.62
31_G	38_Q	0.818	0.61
14_R	19_C	0.798	0.59
13_E	16_C	0.794	0.59
7_L	49_L	0.785	0.58
12_P	28_L	0.777	0.57
15_I	24_P	0.770	0.56
9_P	23_C	0.745	0.54
34_S	37_T	0.744	0.54
9_P	48_W	0.728	0.52
11_H	15_I	0.695	0.49
38_Q	43_L	0.692	0.49
16_C	39_H	0.684	0.48
22_Y	31_G	0.682	0.48
8_H	44_F	0.660	0.45
12_P	36_R	0.652	0.45
11_H	19_C	0.646	0.44
13_E	30_C	0.644	0.44
6_P	41_V	0.639	0.43
29_A	38_Q	0.634	0.43
37_T	44_F	0.624	0.42
12_P	17_W	0.623	0.42
4_K	11_H	0.615	0.41
29_A	35_I	0.563	0.36
27_D	31_G	0.560	0.36
21_K	26_D	0.556	0.35
3_K	15_I	0.546	0.35
30_C	36_R	0.546	0.35
26_D	41_V	0.543	0.34
2_A	8_H	0.541	0.34
31_G	37_T	0.534	0.33
23_C	48_W	0.534	0.33
17_W	39_H	0.529	0.33
42_E	47_D	0.525	0.33
26_D	50_E	0.522	0.32
40_P	48_W	0.517	0.32
32_N	38_Q	0.513	0.32
3_K	22_Y	0.511	0.31
20_D	43_L	0.505	0.31
20_D	49_L	0.500	0.30

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
1gqiA	2	0.3333	6.9	0.921	Contact Map
1j3gA	1	0.6863	4.3	0.928	Contact Map
4uquA	2	0.9216	4.1	0.929	Contact Map
2hw2A	1	0.5686	3.6	0.93	Contact Map
3nzpA	2	0.9804	2.9	0.934	Contact Map
4knkA	1	0.902	2.5	0.936	Contact Map
2i1sA	1	0.9412	2.3	0.938	Contact Map
4ivvA	1	0.902	2.1	0.939	Contact Map
3m97X	1	0.2157	2.1	0.939	Contact Map
4r43A	1	0.9216	2	0.939	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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