DUF1279 - PFAM28P - GREMLIN Contacts

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DUF1279 - Protein of unknown function (DUF1279)

PFAM:	PF06916	Sequences: QRLKKLLKKYGWVALGVYLGLSLVSFGGCYLAVSSGVDVAALLEKVGLSVGSAESATESLKASLAGTFALAYAIHKALAPVRVPLTLALTPK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	92 (88)
Sequences:	950 (672)
Seq/√Len:	71.6
META:	0.378

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_F	68_F	4.629	1.00
25_S	75_H	3.659	1.00
20_G	24_V	2.935	1.00
6_L	14_A	2.523	1.00
12_W	16_G	2.475	1.00
22_S	75_H	2.474	1.00
80_P	84_P	2.394	1.00
34_S	67_T	2.170	1.00
22_S	72_Y	2.106	1.00
19_L	23_L	2.027	1.00
17_V	89_L	1.971	1.00
72_Y	75_H	1.895	1.00
18_Y	79_A	1.778	1.00
30_Y	64_L	1.750	1.00
29_C	33_V	1.748	1.00
22_S	79_A	1.746	1.00
6_L	87_L	1.673	1.00
18_Y	83_V	1.585	0.99
22_S	25_S	1.577	0.99
73_A	78_L	1.512	0.99
11_G	16_G	1.509	0.99
17_V	76_K	1.392	0.98
5_K	9_K	1.388	0.98
14_A	18_Y	1.240	0.96
27_G	31_L	1.234	0.96
22_S	76_K	1.234	0.96
3_L	14_A	1.218	0.96
21_L	25_S	1.188	0.95
38_D	41_A	1.123	0.94
48_L	70_L	1.113	0.94
70_L	73_A	1.111	0.94
41_A	45_K	1.108	0.93
41_A	44_E	1.107	0.93
14_A	86_T	1.098	0.93
23_L	27_G	1.089	0.93
30_Y	66_G	1.085	0.93
18_Y	25_S	1.081	0.93
43_L	48_L	1.075	0.92
76_K	79_A	1.063	0.92
78_L	81_V	1.051	0.91
88_A	91_P	1.023	0.90
79_A	83_V	1.017	0.90
33_V	70_L	0.979	0.88
74_I	78_L	0.968	0.88
6_L	13_V	0.964	0.88
85_L	89_L	0.948	0.87
55_S	58_E	0.936	0.86
13_V	90_T	0.920	0.85
11_G	91_P	0.909	0.84
42_L	45_K	0.885	0.83
9_K	12_W	0.882	0.82
77_A	80_P	0.875	0.82
53_A	56_A	0.872	0.82
72_Y	78_L	0.869	0.81
7_L	14_A	0.864	0.81
7_L	15_L	0.864	0.81
29_C	78_L	0.823	0.78
32_A	48_L	0.820	0.78
18_Y	86_T	0.815	0.77
66_G	69_A	0.813	0.77
8_K	88_A	0.813	0.77
21_L	27_G	0.806	0.76
40_A	45_K	0.792	0.75
87_L	90_T	0.791	0.75
55_S	61_K	0.788	0.75
84_P	88_A	0.784	0.74
53_A	57_T	0.772	0.73
29_C	75_H	0.769	0.73
42_L	65_A	0.760	0.72
25_S	78_L	0.751	0.71
65_A	69_A	0.746	0.71
36_G	72_Y	0.738	0.70
37_V	71_A	0.730	0.69
26_F	71_A	0.730	0.69
54_E	57_T	0.727	0.69
32_A	35_S	0.725	0.68
44_E	47_G	0.722	0.68
31_L	35_S	0.714	0.67
43_L	47_G	0.705	0.66
82_R	86_T	0.703	0.66
18_Y	85_L	0.702	0.66
24_V	85_L	0.698	0.65
55_S	59_S	0.684	0.64
22_S	82_R	0.677	0.63
83_V	87_L	0.677	0.63
75_H	83_V	0.670	0.62
3_L	12_W	0.666	0.62
15_L	44_E	0.665	0.62
2_R	59_S	0.661	0.61
14_A	91_P	0.653	0.60
2_R	8_K	0.652	0.60
44_E	49_S	0.646	0.60
77_A	84_P	0.644	0.59
42_L	46_V	0.643	0.59
2_R	5_K	0.639	0.59
32_A	63_S	0.629	0.57
33_V	75_H	0.627	0.57
46_V	77_A	0.627	0.57
18_Y	76_K	0.620	0.56
40_A	61_K	0.619	0.56
6_L	12_W	0.616	0.56
17_V	91_P	0.614	0.56
73_A	90_T	0.610	0.55
8_K	32_A	0.604	0.54
71_A	75_H	0.600	0.54
20_G	23_L	0.595	0.53
16_G	19_L	0.586	0.52
61_K	81_V	0.578	0.51
84_P	89_L	0.575	0.51
29_C	74_I	0.575	0.51
54_E	58_E	0.573	0.51
56_A	59_S	0.570	0.50
10_Y	81_V	0.564	0.50
39_V	42_L	0.563	0.49
24_V	28_G	0.561	0.49
35_S	81_V	0.553	0.48
55_S	60_L	0.541	0.47
36_G	75_H	0.538	0.46
19_L	72_Y	0.537	0.46
46_V	88_A	0.535	0.46
30_Y	34_S	0.530	0.45
31_L	44_E	0.529	0.45
19_L	52_S	0.529	0.45
7_L	12_W	0.517	0.44
33_V	82_R	0.517	0.44
70_L	83_V	0.514	0.43
59_S	63_S	0.510	0.43
47_G	66_G	0.509	0.43
22_S	33_V	0.506	0.43
19_L	24_V	0.505	0.42
75_H	79_A	0.504	0.42
25_S	66_G	0.500	0.42

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
2zdjA	1	0.7391	9.1	0.893	Contact Map
2zjsY	2	0.9239	6.6	0.9	Contact Map
3j01A	1	0.8804	6.2	0.901	Contact Map
3vn0A	2	0.163	5.2	0.904	Contact Map
3dl8G	1	0.9239	4.8	0.906	Contact Map
2jbwA	2	0.9565	3.8	0.911	Contact Map
1lnsA	2	0.9674	3.7	0.911	Contact Map
2b9vA	5	0.9674	3.7	0.911	Contact Map
1ytrA	1	0.1304	3.6	0.911	Contact Map
1mpxA	4	0.9674	3.4	0.912	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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