DUF3311 - PFAM28P - GREMLIN Contacts

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DUF3311 - Protein of unknown function (DUF3311)

PFAM:	PF11755	Sequences: WLLLIPFFVALLWVPFYNRVEPLLFGLPFFYWYQLLWVLLTALLTALVYRLTRRRRRERRG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	61 (54)
Sequences:	8645 (4575)
Seq/√Len:	622.6
META:	0.905

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_V	23_L	3.143	1.00
46_A	50_R	2.870	1.00
24_L	32_W	2.606	1.00
13_W	16_F	2.497	1.00
32_W	36_L	2.362	1.00
39_L	43_L	1.740	1.00
17_Y	29_F	1.686	1.00
33_Y	37_W	1.622	1.00
47_L	51_L	1.610	1.00
2_L	6_P	1.552	1.00
8_F	11_L	1.499	1.00
29_F	33_Y	1.485	1.00
50_R	53_R	1.462	1.00
10_A	33_Y	1.444	1.00
39_L	42_A	1.421	1.00
10_A	37_W	1.326	1.00
42_A	46_A	1.269	1.00
19_R	22_P	1.262	1.00
45_T	49_Y	1.203	1.00
41_T	45_T	1.163	1.00
22_P	29_F	1.146	1.00
45_T	48_V	1.142	1.00
19_R	29_F	1.119	1.00
53_R	56_R	1.099	1.00
30_F	34_Q	1.090	1.00
23_L	32_W	1.052	1.00
17_Y	30_F	1.027	1.00
38_V	45_T	1.023	1.00
36_L	40_L	1.022	1.00
27_L	35_L	0.973	1.00
48_V	52_T	0.953	1.00
45_T	52_T	0.922	1.00
46_A	49_Y	0.916	1.00
6_P	11_L	0.871	1.00
38_V	41_T	0.849	1.00
9_V	37_W	0.842	1.00
43_L	47_L	0.840	1.00
11_L	16_F	0.838	1.00
8_F	12_L	0.833	1.00
5_I	44_L	0.828	1.00
11_L	37_W	0.827	1.00
14_V	18_N	0.818	1.00
3_L	6_P	0.814	1.00
13_W	17_Y	0.811	1.00
44_L	47_L	0.774	1.00
52_T	55_R	0.756	1.00
37_W	40_L	0.738	1.00
31_Y	41_T	0.733	1.00
12_L	16_F	0.726	1.00
2_L	5_I	0.702	1.00
23_L	26_G	0.700	1.00
9_V	12_L	0.697	1.00
25_F	35_L	0.692	1.00
17_Y	31_Y	0.687	1.00
23_L	27_L	0.684	1.00
16_F	33_Y	0.677	1.00
39_L	46_A	0.677	1.00
37_W	44_L	0.661	1.00
49_Y	53_R	0.654	1.00
9_V	13_W	0.650	1.00
35_L	38_V	0.648	1.00
51_L	55_R	0.646	1.00
43_L	46_A	0.644	1.00
6_P	41_T	0.631	1.00
14_V	17_Y	0.623	1.00
10_A	34_Q	0.618	1.00
36_L	39_L	0.616	1.00
49_Y	55_R	0.586	1.00
41_T	47_L	0.582	1.00
31_Y	38_V	0.553	1.00
30_F	35_L	0.548	1.00
17_Y	22_P	0.544	0.99
18_N	35_L	0.541	0.99
42_A	47_L	0.540	0.99
15_P	18_N	0.530	0.99
35_L	39_L	0.526	0.99
34_Q	38_V	0.516	0.99
10_A	38_V	0.512	0.99
17_Y	33_Y	0.510	0.99
22_P	32_W	0.505	0.99
40_L	43_L	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
4httA	1	0.6557	7.4	0.857	Contact Map
4p02A	1	0.9508	6.2	0.862	Contact Map
4b4aA	1	0.6557	6	0.863	Contact Map
4uc1A	3	0.8689	5.6	0.865	Contact Map
2a65A	2	1	4.7	0.87	Contact Map
2xq2A	2	0.9672	4.3	0.872	Contact Map
3dh4A	3	0.9672	4.2	0.873	Contact Map
4c7rA	3	0.918	3.4	0.878	Contact Map
4ogqG	1	0.6066	3.4	0.879	Contact Map
2mgyA	1	0.9508	3.3	0.88	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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