DUF1516 - PFAM28P - GREMLIN Contacts

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DUF1516 - Protein of unknown function (DUF1516)

PFAM:	PF07457	Sequences: THLHITSWVLAIILFFVALFLYKKGKAKGAKIVHMILRLFYLLIIITGIGLLISYFSGFPMLYILKGLLGLWVIGLMEMILVRKKKGKPTKGFWILFIIALILTLYLG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	108 (108)
Sequences:	542 (408)
Seq/√Len:	39.3
META:	0.288

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
72_W	96_L	3.741	1.00
11_A	44_I	2.981	1.00
35_M	39_L	2.662	1.00
34_H	82_V	2.402	1.00
10_L	40_F	2.355	1.00
49_I	53_I	2.346	1.00
32_I	36_I	2.331	1.00
16_F	20_F	2.279	1.00
80_I	94_W	2.250	1.00
96_L	100_A	2.175	0.99
73_V	104_T	2.166	0.99
82_V	86_K	2.022	0.99
3_L	47_T	2.006	0.99
42_L	46_I	1.892	0.98
70_G	73_V	1.891	0.98
92_G	96_L	1.843	0.98
75_G	79_M	1.752	0.97
23_K	84_K	1.745	0.97
17_V	21_L	1.735	0.97
2_H	6_T	1.668	0.96
62_L	107_L	1.655	0.96
7_S	43_L	1.654	0.96
14_L	37_L	1.589	0.95
45_I	75_G	1.563	0.95
80_I	97_F	1.561	0.94
72_W	76_L	1.535	0.94
4_H	48_G	1.469	0.92
52_L	67_G	1.460	0.92
94_W	97_F	1.453	0.92
98_I	102_I	1.440	0.92
91_K	95_I	1.395	0.90
11_A	37_L	1.380	0.90
18_A	33_V	1.380	0.90
76_L	93_F	1.309	0.87
45_I	49_I	1.274	0.86
22_Y	34_H	1.256	0.85
70_G	104_T	1.231	0.84
65_L	68_L	1.211	0.83
72_W	100_A	1.205	0.82
83_R	88_K	1.203	0.82
69_L	104_T	1.190	0.82
46_I	49_I	1.179	0.81
69_L	103_L	1.166	0.80
52_L	63_Y	1.149	0.79
5_I	8_W	1.107	0.77
61_M	64_I	1.106	0.77
52_L	55_Y	1.062	0.74
56_F	60_P	1.056	0.73
1_T	5_I	1.052	0.73
5_I	9_V	1.046	0.72
48_G	66_K	1.040	0.72
64_I	68_L	1.037	0.72
22_Y	30_A	1.033	0.71
15_F	77_M	1.032	0.71
18_A	30_A	1.031	0.71
18_A	81_L	1.030	0.71
76_L	96_L	1.030	0.71
12_I	105_L	1.021	0.71
3_L	6_T	1.000	0.69
69_L	107_L	0.971	0.67
76_L	80_I	0.940	0.64
102_I	106_Y	0.940	0.64
31_K	35_M	0.930	0.63
25_G	31_K	0.920	0.62
13_I	17_V	0.918	0.62
61_M	65_L	0.913	0.62
43_L	47_T	0.908	0.61
76_L	90_T	0.907	0.61
60_P	65_L	0.900	0.61
19_L	84_K	0.857	0.57
69_L	72_W	0.853	0.57
31_K	39_L	0.844	0.56
38_R	78_E	0.839	0.55
34_H	81_L	0.838	0.55
16_F	86_K	0.824	0.54
29_G	33_V	0.819	0.54
40_F	46_I	0.816	0.53
56_F	64_I	0.814	0.53
10_L	71_L	0.789	0.51
4_H	66_K	0.789	0.51
11_A	73_V	0.783	0.50
12_I	16_F	0.783	0.50
6_T	10_L	0.740	0.46
90_T	94_W	0.740	0.46
74_I	80_I	0.732	0.46
5_I	67_G	0.729	0.45
24_K	33_V	0.728	0.45
41_Y	74_I	0.727	0.45
92_G	100_A	0.718	0.44
7_S	19_L	0.716	0.44
59_F	64_I	0.699	0.43
30_A	39_L	0.698	0.43
19_L	71_L	0.696	0.42
21_L	33_V	0.689	0.42
49_I	56_F	0.689	0.42
72_W	79_M	0.687	0.42
44_I	59_F	0.681	0.41
66_K	78_E	0.679	0.41
7_S	10_L	0.679	0.41
80_I	93_F	0.677	0.41
50_G	58_G	0.675	0.41
16_F	106_Y	0.674	0.40
5_I	70_G	0.671	0.40
70_G	78_E	0.671	0.40
75_G	82_V	0.669	0.40
93_F	99_I	0.667	0.40
46_I	50_G	0.663	0.39
77_M	101_L	0.661	0.39
14_L	40_F	0.655	0.39
86_K	89_P	0.653	0.39
65_L	93_F	0.652	0.39
69_L	73_V	0.648	0.38
30_A	34_H	0.646	0.38
52_L	64_I	0.646	0.38
6_T	9_V	0.644	0.38
13_I	89_P	0.639	0.37
39_L	42_L	0.637	0.37
92_G	106_Y	0.637	0.37
16_F	99_I	0.636	0.37
51_L	66_K	0.634	0.37
66_K	70_G	0.630	0.37
84_K	98_I	0.622	0.36
29_G	32_I	0.621	0.36
62_L	103_L	0.620	0.36
53_I	56_F	0.612	0.35
68_L	71_L	0.610	0.35
75_G	93_F	0.606	0.35
76_L	100_A	0.604	0.35
28_K	72_W	0.602	0.34
30_A	84_K	0.600	0.34
28_K	32_I	0.599	0.34
99_I	103_L	0.598	0.34
44_I	83_R	0.597	0.34
13_I	79_M	0.594	0.34
16_F	42_L	0.592	0.34
44_I	70_G	0.589	0.33
80_I	95_I	0.575	0.32
68_L	106_Y	0.570	0.32
79_M	82_V	0.567	0.32
5_I	44_I	0.565	0.31
40_F	43_L	0.563	0.31
52_L	56_F	0.562	0.31
80_I	90_T	0.556	0.31
55_Y	59_F	0.550	0.30
62_L	65_L	0.544	0.30
49_I	61_M	0.536	0.29
20_F	98_I	0.531	0.29
97_F	102_I	0.527	0.28
11_A	70_G	0.525	0.28
22_Y	84_K	0.524	0.28
32_I	85_K	0.517	0.28
79_M	83_R	0.515	0.28
69_L	100_A	0.514	0.28
39_L	69_L	0.513	0.27
27_A	30_A	0.511	0.27
37_L	81_L	0.508	0.27
76_L	103_L	0.506	0.27
66_K	108_G	0.505	0.27
17_V	33_V	0.505	0.27
27_A	71_L	0.503	0.27
15_F	40_F	0.502	0.27
43_L	70_G	0.500	0.27

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
4p02A	1	0.8889	3.4	0.925	Contact Map
4hfiA	3	0.5278	2.9	0.927	Contact Map
1skhA	1	0.2685	2.6	0.929	Contact Map
4o6yA	2	1	2.1	0.932	Contact Map
4xp4A	1	0.7222	2	0.933	Contact Map
3pjzA	2	0.713	2	0.933	Contact Map
2l2tA	2	0.3704	1.4	0.938	Contact Map
4u2pA	4	0.1944	1.4	0.938	Contact Map
2jwaA	2	0.3981	1.4	0.939	Contact Map
4fbzA	3	0.5185	1.4	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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