DUF3098 - PFAM28P - GREMLIN Contacts

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DUF3098 - Protein of unknown function (DUF3098)

PFAM:	PF11297	Sequences: AFGKENYILMLIGLAVIILGFILMSGGGSDDPNVFNPEIFSFRRITLAPILILAGFVIEIYAIMKKP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	67 (66)
Sequences:	6907 (3363)
Seq/√Len:	413.9
META:	0.949

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
42_F	47_L	3.628	1.00
13_G	59_E	2.990	1.00
5_E	65_K	2.491	1.00
31_D	34_V	2.337	1.00
16_V	58_I	2.243	1.00
11_L	15_A	2.151	1.00
4_K	8_I	2.013	1.00
5_E	8_I	1.758	1.00
13_G	58_I	1.688	1.00
23_L	51_L	1.623	1.00
8_I	12_I	1.615	1.00
46_T	50_I	1.537	1.00
42_F	46_T	1.535	1.00
17_I	21_F	1.411	1.00
15_A	19_L	1.409	1.00
24_M	52_I	1.409	1.00
16_V	54_A	1.402	1.00
22_I	25_S	1.378	1.00
50_I	54_A	1.326	1.00
59_E	62_A	1.281	1.00
17_I	56_F	1.264	1.00
53_L	57_V	1.263	1.00
10_M	59_E	1.258	1.00
21_F	52_I	1.234	1.00
10_M	62_A	1.227	1.00
54_A	58_I	1.192	1.00
61_Y	65_K	1.185	1.00
38_E	41_S	1.173	1.00
9_L	65_K	1.168	1.00
9_L	58_I	1.156	1.00
16_V	51_L	1.151	1.00
56_F	59_E	1.146	1.00
26_G	44_R	1.105	1.00
29_S	35_F	1.059	1.00
5_E	9_L	1.037	1.00
57_V	61_Y	1.036	1.00
41_S	45_I	1.021	1.00
3_G	65_K	1.015	1.00
60_I	64_M	1.014	1.00
58_I	61_Y	1.001	1.00
48_A	52_I	0.966	1.00
29_S	34_V	0.965	1.00
41_S	44_R	0.960	1.00
1_A	40_F	0.954	1.00
17_I	59_E	0.952	1.00
43_R	47_L	0.924	1.00
21_F	64_M	0.885	1.00
29_S	38_E	0.874	1.00
30_D	38_E	0.866	1.00
8_I	11_L	0.838	1.00
1_A	4_K	0.822	1.00
19_L	22_I	0.795	1.00
9_L	12_I	0.785	1.00
24_M	45_I	0.764	1.00
9_L	62_A	0.741	1.00
11_L	14_L	0.728	1.00
34_V	37_P	0.726	1.00
14_L	18_I	0.722	1.00
30_D	34_V	0.710	1.00
12_I	15_A	0.709	1.00
2_F	7_Y	0.690	1.00
29_S	36_N	0.676	1.00
27_G	30_D	0.675	1.00
44_R	48_A	0.661	0.99
2_F	10_M	0.651	0.99
33_N	37_P	0.640	0.99
2_F	6_N	0.635	0.99
20_G	52_I	0.630	0.99
18_I	22_I	0.628	0.99
23_L	43_R	0.624	0.99
17_I	52_I	0.615	0.99
27_G	43_R	0.612	0.99
40_F	44_R	0.593	0.99
54_A	57_V	0.589	0.99
3_G	6_N	0.587	0.99
36_N	39_I	0.587	0.99
40_F	45_I	0.580	0.99
6_N	62_A	0.580	0.99
12_I	58_I	0.571	0.98
21_F	56_F	0.568	0.98
19_L	23_L	0.559	0.98
30_D	33_N	0.559	0.98
29_S	40_F	0.552	0.98
12_I	16_V	0.544	0.98
35_F	39_I	0.533	0.97
19_L	51_L	0.530	0.97
12_I	19_L	0.529	0.97
13_G	62_A	0.529	0.97
19_L	47_L	0.528	0.97
27_G	41_S	0.524	0.97
26_G	43_R	0.522	0.97
24_M	48_A	0.520	0.97
9_L	61_Y	0.517	0.97
5_E	61_Y	0.516	0.97
3_G	7_Y	0.512	0.97
35_F	38_E	0.509	0.97
55_G	62_A	0.507	0.97
51_L	59_E	0.503	0.96
37_P	40_F	0.500	0.96

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
2gsmB	1	1	7.4	0.891	Contact Map
2mmuA	1	0.3881	6.6	0.893	Contact Map
3hb3B	1	1	6.4	0.894	Contact Map
3ixzA	1	0.8955	5.6	0.897	Contact Map
2zxeA	1	0.8955	5.6	0.897	Contact Map
3b5dA	2	0.4179	5.4	0.897	Contact Map
3ayfA	2	0.9403	4.1	0.903	Contact Map
4phuA	1	0.4179	3.7	0.905	Contact Map
2yevB	1	1	3.6	0.906	Contact Map
3mk7A	1	0.9104	3.5	0.907	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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