DUF3078 - PFAM28P - GREMLIN Contacts

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DUF3078 - Protein of unknown function (DUF3078)

PFAM:	PF11276	Sequences: FSQSSFSNWAAGGENSLSLNGLLNLFANYKKGKFSWDNSLDLAYGLVKQGDQLDGFRKTDDRIDLNSKYGYKASKKWYYSALLNFRTQFANGY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	93 (91)
Sequences:	9780 (6093)
Seq/√Len:	638.7
META:	0.935

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_F	69_Y	4.661	1.00
44_Y	90_A	3.086	1.00
73_A	79_Y	2.532	1.00
43_A	60_D	2.479	1.00
36_W	67_S	2.198	1.00
42_L	89_F	2.069	1.00
33_K	71_Y	2.036	1.00
28_N	37_D	1.929	1.00
38_N	67_S	1.884	1.00
64_D	84_N	1.879	1.00
30_K	72_K	1.652	1.00
24_N	41_D	1.617	1.00
34_F	71_Y	1.611	1.00
35_S	78_Y	1.595	1.00
64_D	86_R	1.567	1.00
46_L	56_F	1.508	1.00
72_K	78_Y	1.498	1.00
42_L	63_I	1.458	1.00
26_F	39_S	1.446	1.00
74_S	77_W	1.440	1.00
41_D	62_R	1.416	1.00
52_Q	57_R	1.312	1.00
20_N	60_D	1.305	1.00
63_I	87_T	1.289	1.00
31_K	34_F	1.288	1.00
43_A	62_R	1.257	1.00
58_K	61_D	1.248	1.00
30_K	35_S	1.239	1.00
47_V	59_T	1.225	1.00
40_L	65_L	1.218	1.00
29_Y	34_F	1.191	1.00
14_E	49_Q	1.185	1.00
61_D	89_F	1.177	1.00
58_K	88_Q	1.150	1.00
66_N	84_N	1.130	1.00
69_Y	81_A	1.121	1.00
37_D	68_K	1.111	1.00
6_F	13_G	1.101	1.00
49_Q	52_Q	1.099	1.00
48_K	55_G	1.082	1.00
1_F	17_L	1.076	1.00
68_K	82_L	1.057	1.00
48_K	56_F	1.037	1.00
20_N	43_A	1.013	1.00
72_K	75_K	1.006	1.00
66_N	82_L	0.996	1.00
6_F	15_N	0.993	1.00
22_L	41_D	0.993	1.00
19_L	46_L	0.992	1.00
14_E	57_R	0.982	1.00
41_D	64_D	0.978	1.00
14_E	50_G	0.977	1.00
27_A	40_L	0.976	1.00
39_S	66_N	0.976	1.00
24_N	39_S	0.951	1.00
28_N	39_S	0.934	1.00
63_I	89_F	0.930	1.00
33_K	72_K	0.929	1.00
49_Q	57_R	0.928	1.00
25_L	40_L	0.924	1.00
67_S	83_L	0.921	1.00
61_D	88_Q	0.904	1.00
70_G	78_Y	0.902	1.00
45_G	59_T	0.900	1.00
20_N	45_G	0.899	1.00
35_S	70_G	0.897	1.00
46_L	90_A	0.894	1.00
28_N	38_N	0.881	1.00
38_N	65_L	0.880	1.00
88_Q	92_G	0.865	1.00
51_D	55_G	0.858	1.00
2_S	20_N	0.855	1.00
70_G	80_S	0.853	1.00
2_S	18_S	0.834	1.00
21_G	42_L	0.825	1.00
36_W	69_Y	0.824	1.00
5_S	15_N	0.822	1.00
45_G	58_K	0.815	1.00
29_Y	32_G	0.811	1.00
27_A	65_L	0.810	1.00
15_N	50_G	0.809	1.00
52_Q	55_G	0.774	1.00
30_K	37_D	0.761	1.00
33_K	73_A	0.759	1.00
37_D	70_G	0.750	1.00
22_L	43_A	0.740	1.00
3_Q	17_L	0.739	1.00
21_G	25_L	0.738	1.00
12_G	16_S	0.721	1.00
11_A	58_K	0.720	1.00
35_S	68_K	0.715	1.00
58_K	92_G	0.712	1.00
68_K	80_S	0.694	1.00
82_L	86_R	0.680	1.00
37_D	78_Y	0.675	1.00
28_N	35_S	0.673	1.00
79_Y	83_L	0.669	1.00
48_K	52_Q	0.668	1.00
47_V	57_R	0.667	1.00
63_I	85_F	0.663	1.00
4_S	18_S	0.662	1.00
18_S	47_V	0.660	1.00
26_F	37_D	0.654	1.00
14_E	52_Q	0.650	1.00
27_A	38_N	0.637	1.00
17_L	48_K	0.635	1.00
39_S	64_D	0.633	1.00
72_K	76_K	0.630	1.00
64_D	82_L	0.628	1.00
75_K	78_Y	0.611	1.00
35_S	72_K	0.592	1.00
52_Q	56_F	0.581	1.00
73_A	78_Y	0.581	1.00
45_G	92_G	0.579	1.00
4_S	16_S	0.579	1.00
74_S	78_Y	0.574	1.00
19_L	23_L	0.558	1.00
24_N	27_A	0.554	1.00
77_W	80_S	0.554	1.00
43_A	82_L	0.553	1.00
34_F	79_Y	0.551	1.00
71_Y	79_Y	0.549	1.00
65_L	85_F	0.548	1.00
18_S	59_T	0.534	0.99
13_G	18_S	0.534	0.99
57_R	92_G	0.531	0.99
14_E	51_D	0.529	0.99
66_N	80_S	0.529	0.99
9_W	87_T	0.514	0.99
38_N	42_L	0.514	0.99
42_L	90_A	0.513	0.99
4_S	13_G	0.511	0.99
81_A	85_F	0.510	0.99
10_A	14_E	0.506	0.99
50_G	56_F	0.506	0.99
85_F	88_Q	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
2x9kA	1	0.9785	7.5	0.888	Contact Map
3k63A	1	0.4409	4.8	0.898	Contact Map
4rl8A	3	0.9247	4.5	0.899	Contact Map
2krtA	1	0.4946	3.8	0.903	Contact Map
3nb3A	2	0.8602	2.1	0.915	Contact Map
3qraA	1	0.6237	1.2	0.927	Contact Map
1ormA	1	0.5591	1.2	0.927	Contact Map
4x1cC	5	0.2258	1	0.929	Contact Map
4fqeA	1	0.7204	0.9	0.931	Contact Map
1ajoA	1	0.9785	0.9	0.931	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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