DUF3110 - PFAM28P - GREMLIN Contacts

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DUF3110 - Protein of unknown function (DUF3110)

PFAM:	PF11360	Sequences: VYVLLFNAGKEDEGAYSVQDDGEKVVLLFEEEDDAERYAMMLEAQDFPEMTVIEVDDEEIIKTCEMHGYKYAIITPNDIVIPPE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	84 (76)
Sequences:	1873 (1033)
Seq/√Len:	118.4
META:	0.913

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_E	76_P	3.589	1.00
62_K	66_M	3.282	1.00
75_T	78_D	3.105	1.00
41_M	44_A	2.774	1.00
24_K	27_L	2.717	1.00
40_M	43_E	2.533	1.00
28_L	60_I	2.432	1.00
32_E	36_E	2.201	1.00
23_E	27_L	2.134	1.00
78_D	81_I	1.914	1.00
57_D	61_I	1.881	1.00
30_E	76_P	1.824	1.00
40_M	44_A	1.745	1.00
36_E	40_M	1.620	1.00
23_E	26_V	1.573	1.00
56_D	59_E	1.551	1.00
61_I	71_Y	1.540	1.00
42_L	47_F	1.517	1.00
30_E	75_T	1.512	1.00
59_E	63_T	1.476	1.00
33_D	36_E	1.437	1.00
41_M	81_I	1.401	1.00
15_A	63_T	1.373	1.00
58_E	62_K	1.342	1.00
23_E	70_K	1.325	1.00
71_Y	81_I	1.262	0.99
11_E	51_T	1.209	0.99
17_S	60_I	1.181	0.99
28_L	69_Y	1.149	0.99
19_Q	22_G	1.106	0.99
59_E	62_K	1.077	0.98
26_V	69_Y	1.050	0.98
28_L	73_I	1.013	0.97
12_D	60_I	0.967	0.97
25_V	72_A	0.954	0.96
61_I	65_E	0.952	0.96
17_S	48_P	0.928	0.96
33_D	46_D	0.914	0.95
29_F	35_A	0.895	0.95
18_V	27_L	0.890	0.95
35_A	69_Y	0.886	0.95
34_D	37_R	0.885	0.94
71_Y	78_D	0.867	0.94
15_A	60_I	0.863	0.94
38_Y	78_D	0.855	0.93
28_L	71_Y	0.853	0.93
38_Y	81_I	0.838	0.93
58_E	65_E	0.830	0.92
14_G	17_S	0.822	0.92
31_E	65_E	0.813	0.92
57_D	63_T	0.806	0.91
9_G	12_D	0.803	0.91
54_E	71_Y	0.798	0.91
47_F	70_K	0.793	0.91
18_V	83_P	0.780	0.90
27_L	60_I	0.757	0.88
28_L	62_K	0.755	0.88
33_D	37_R	0.755	0.88
55_V	60_I	0.751	0.88
10_K	13_E	0.748	0.88
19_Q	47_F	0.739	0.87
18_V	80_V	0.735	0.87
73_I	78_D	0.729	0.86
63_T	69_Y	0.712	0.85
9_G	17_S	0.711	0.85
78_D	83_P	0.708	0.85
45_Q	53_I	0.703	0.84
11_E	21_D	0.697	0.84
35_A	52_V	0.695	0.84
56_D	72_A	0.692	0.84
75_T	79_I	0.659	0.80
9_G	48_P	0.658	0.80
52_V	55_V	0.657	0.80
13_E	50_M	0.656	0.80
28_L	57_D	0.648	0.79
26_V	38_Y	0.645	0.79
8_A	60_I	0.636	0.78
53_I	60_I	0.634	0.78
76_P	79_I	0.626	0.77
56_D	78_D	0.620	0.76
26_V	63_T	0.614	0.76
43_E	48_P	0.614	0.76
18_V	77_N	0.613	0.75
47_F	59_E	0.612	0.75
32_E	54_E	0.610	0.75
26_V	71_Y	0.610	0.75
31_E	78_D	0.597	0.74
51_T	56_D	0.591	0.73
71_Y	80_V	0.589	0.73
53_I	59_E	0.589	0.73
51_T	55_V	0.570	0.70
54_E	73_I	0.569	0.70
15_A	26_V	0.566	0.70
27_L	47_F	0.566	0.70
62_K	65_E	0.561	0.69
16_Y	45_Q	0.555	0.68
37_R	41_M	0.550	0.67
13_E	58_E	0.546	0.67
37_R	79_I	0.542	0.66
32_E	49_E	0.540	0.66
63_T	67_H	0.536	0.65
18_V	38_Y	0.531	0.65
15_A	50_M	0.525	0.64
48_P	68_G	0.525	0.64
16_Y	19_Q	0.523	0.64
53_I	67_H	0.523	0.64
17_S	43_E	0.520	0.63
14_G	33_D	0.512	0.62
58_E	75_T	0.512	0.62
16_Y	22_G	0.508	0.61
30_E	58_E	0.506	0.61
60_I	67_H	0.506	0.61
57_D	74_I	0.505	0.61
9_G	15_A	0.500	0.60

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
4e6zA	1	0.9524	74.2	0.84	Contact Map
4ev1A	2	0.9524	71.1	0.844	Contact Map
2jyaA	1	0.6429	35.7	0.874	Contact Map
2ljuA	1	0.7024	35.5	0.874	Contact Map
4wkgA	5	0.9524	25.6	0.883	Contact Map
2blnA	1	0.9286	17.1	0.892	Contact Map
4dixA	1	0.6905	14.7	0.896	Contact Map
2hiqA	2	0.5476	14.6	0.896	Contact Map
1tueB	1	0.5238	13.4	0.897	Contact Map
2asyA	2	0.6786	12	0.899	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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