DUF3817 - PFAM28P - GREMLIN Contacts

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DUF3817 - Domain of unknown function (DUF3817)

PFAM:	PF12823	Sequences: LKRFRVIAILEGVSLLLLFVAMPLKYLAVKIVGMIHGVLFIAYLVLALLLARRLRWSLKRTLLALLASLIPFGTFVVERKLRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	83 (81)
Sequences:	10496 (6380)
Seq/√Len:	708.9
META:	0.829

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_A	61_T	3.663	1.00
34_M	38_V	2.642	1.00
64_A	77_V	2.429	1.00
30_K	34_M	2.417	1.00
49_L	53_R	2.104	1.00
23_P	27_L	2.103	1.00
19_F	23_P	2.089	1.00
3_R	49_L	1.987	1.00
22_M	26_Y	1.969	1.00
48_L	52_R	1.917	1.00
47_A	64_A	1.904	1.00
2_K	6_V	1.689	1.00
56_W	60_R	1.504	1.00
21_A	28_A	1.464	1.00
20_V	24_L	1.452	1.00
57_S	60_R	1.447	1.00
17_L	32_V	1.440	1.00
14_S	39_L	1.431	1.00
28_A	31_I	1.392	1.00
20_V	23_P	1.371	1.00
41_I	45_V	1.324	1.00
7_I	42_A	1.297	1.00
45_V	49_L	1.289	1.00
7_I	46_L	1.266	1.00
31_I	34_M	1.255	1.00
73_G	76_V	1.239	1.00
16_L	72_F	1.233	1.00
50_L	54_L	1.232	1.00
21_A	29_V	1.211	1.00
3_R	46_L	1.169	1.00
28_A	32_V	1.125	1.00
3_R	6_V	1.114	1.00
9_I	13_V	1.095	1.00
58_L	62_L	1.095	1.00
2_K	5_R	1.078	1.00
52_R	55_R	1.066	1.00
47_A	61_T	1.041	1.00
6_V	10_L	1.040	1.00
47_A	65_L	1.039	1.00
8_A	74_T	1.018	1.00
38_V	41_I	1.018	1.00
29_V	33_G	1.011	1.00
59_K	63_L	1.002	1.00
13_V	17_L	0.999	1.00
19_F	22_M	0.985	1.00
4_F	50_L	0.979	1.00
18_L	33_G	0.978	1.00
25_K	29_V	0.970	1.00
31_I	35_I	0.954	1.00
49_L	52_R	0.953	1.00
79_R	82_R	0.950	1.00
21_A	32_V	0.942	1.00
40_F	68_S	0.937	1.00
74_T	77_V	0.936	1.00
5_R	78_E	0.936	1.00
76_V	80_K	0.905	1.00
63_L	80_K	0.904	1.00
10_L	39_L	0.880	1.00
38_V	42_A	0.877	1.00
44_L	65_L	0.871	1.00
21_A	25_K	0.862	1.00
67_A	77_V	0.854	1.00
3_R	7_I	0.849	1.00
72_F	76_V	0.845	1.00
12_G	74_T	0.840	1.00
51_A	56_W	0.840	1.00
23_P	26_Y	0.838	1.00
5_R	9_I	0.831	1.00
4_F	43_Y	0.831	1.00
51_A	54_L	0.830	1.00
22_M	32_V	0.826	1.00
64_A	81_L	0.816	1.00
77_V	81_L	0.809	1.00
18_L	21_A	0.804	1.00
12_G	75_F	0.795	1.00
13_V	75_F	0.792	1.00
4_F	8_A	0.791	1.00
24_L	27_L	0.790	1.00
51_A	58_L	0.788	1.00
44_L	48_L	0.780	1.00
50_L	53_R	0.777	1.00
76_V	81_L	0.742	1.00
46_L	49_L	0.730	1.00
59_K	62_L	0.718	1.00
32_V	35_I	0.712	1.00
67_A	74_T	0.709	1.00
11_E	14_S	0.702	1.00
62_L	66_L	0.694	1.00
24_L	28_A	0.692	1.00
43_Y	64_A	0.687	1.00
11_E	39_L	0.687	1.00
22_M	25_K	0.632	1.00
60_R	80_K	0.623	1.00
51_A	57_S	0.612	1.00
69_L	74_T	0.606	1.00
74_T	78_E	0.599	1.00
63_L	77_V	0.578	1.00
14_S	33_G	0.577	1.00
4_F	47_A	0.574	1.00
15_L	19_F	0.574	1.00
51_A	55_R	0.568	1.00
44_L	61_T	0.563	1.00
62_L	65_L	0.560	1.00
3_R	42_A	0.560	1.00
35_I	39_L	0.553	1.00
21_A	24_L	0.549	1.00
61_T	65_L	0.546	1.00
50_L	64_A	0.546	1.00
8_A	67_A	0.539	1.00
5_R	82_R	0.539	1.00
21_A	31_I	0.539	1.00
18_L	29_V	0.536	1.00
33_G	38_V	0.530	1.00
9_I	78_E	0.530	1.00
15_L	74_T	0.522	1.00
43_Y	67_A	0.516	1.00
50_L	56_W	0.515	1.00
22_M	29_V	0.511	0.99
17_L	28_A	0.508	0.99
55_R	59_K	0.503	0.99
15_L	69_L	0.502	0.99
19_F	26_Y	0.500	0.99

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
2k44A	1	0.1325	1.3	0.926	Contact Map
4he8M	1	1	1.3	0.927	Contact Map
3rkoM	1	1	1.2	0.929	Contact Map
3rkoN	1	1	1.1	0.929	Contact Map
2xndJ	3	0.3133	1	0.931	Contact Map
4ff5A	1	0	1	0.931	Contact Map
4f4sA	3	0.3253	1	0.932	Contact Map
2qtsA	4	0.3614	1	0.933	Contact Map
1zrvA	1	0.1566	0.9	0.933	Contact Map
2xgrA	1	0.0241	0.9	0.934	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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