DUF1656 - PFAM28P - GREMLIN Contacts

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DUF1656 - Protein of unknown function (DUF1656)

PFAM:	PF07869	Sequences: EIDLGGVYVPPLLLLAVLALLLTLLLRRLLARLGLYRYVWHPALFDLALYVILLGL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	56 (55)
Sequences:	5305 (2921)
Seq/√Len:	393.9
META:	0.835

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_L	53_L	3.103	1.00
39_V	45_F	2.861	1.00
15_L	54_L	2.493	1.00
50_Y	54_L	2.205	1.00
3_D	6_G	2.158	1.00
12_L	54_L	2.127	1.00
30_L	35_L	1.973	1.00
27_R	46_D	1.832	1.00
22_L	53_L	1.811	1.00
19_A	54_L	1.737	1.00
16_A	50_Y	1.609	1.00
36_Y	46_D	1.585	1.00
10_P	13_L	1.510	1.00
40_W	45_F	1.492	1.00
24_L	27_R	1.481	1.00
29_L	33_L	1.477	1.00
2_I	14_L	1.461	1.00
11_P	15_L	1.383	1.00
19_A	23_T	1.280	1.00
3_D	8_Y	1.252	1.00
41_H	44_L	1.238	1.00
28_R	32_R	1.218	1.00
35_L	39_V	1.195	1.00
45_F	48_A	1.116	1.00
19_A	50_Y	1.051	1.00
30_L	49_L	1.045	1.00
1_E	10_P	1.023	1.00
31_A	42_P	1.015	1.00
46_D	50_Y	0.988	1.00
16_A	54_L	0.932	1.00
23_T	46_D	0.913	1.00
16_A	27_R	0.897	1.00
31_A	36_Y	0.865	1.00
15_L	19_A	0.859	1.00
42_P	46_D	0.856	1.00
19_A	53_L	0.851	1.00
12_L	36_Y	0.827	1.00
1_E	11_P	0.815	1.00
35_L	38_Y	0.811	1.00
40_W	44_L	0.808	1.00
9_V	14_L	0.762	1.00
40_W	48_A	0.755	1.00
20_L	50_Y	0.741	1.00
25_L	28_R	0.740	1.00
23_T	27_R	0.740	1.00
22_L	32_R	0.714	1.00
25_L	39_V	0.711	1.00
7_V	12_L	0.688	0.99
26_L	49_L	0.687	0.99
29_L	34_G	0.673	0.99
34_G	37_R	0.669	0.99
13_L	17_V	0.663	0.99
34_G	45_F	0.661	0.99
33_L	38_Y	0.655	0.99
17_V	21_L	0.647	0.99
51_V	55_G	0.620	0.99
10_P	43_A	0.619	0.99
10_P	54_L	0.615	0.99
42_P	55_G	0.615	0.99
28_R	31_A	0.614	0.99
8_Y	52_I	0.612	0.99
33_L	36_Y	0.612	0.99
25_L	29_L	0.607	0.99
24_L	31_A	0.598	0.99
15_L	23_T	0.598	0.99
36_Y	42_P	0.596	0.99
27_R	31_A	0.595	0.99
21_L	25_L	0.585	0.98
7_V	11_P	0.576	0.98
8_Y	14_L	0.570	0.98
3_D	48_A	0.561	0.98
10_P	15_L	0.549	0.98
36_Y	47_L	0.544	0.97
15_L	18_L	0.538	0.97
1_E	8_Y	0.538	0.97
2_I	5_G	0.525	0.97
5_G	8_Y	0.521	0.97
8_Y	54_L	0.517	0.96
12_L	15_L	0.507	0.96
45_F	51_V	0.503	0.96
18_L	21_L	0.502	0.96
36_Y	39_V	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
3wguB	1	0.5893	4.4	0.856	Contact Map
2zxeB	1	0.2321	4.3	0.856	Contact Map
2hi7B	1	0.3214	2.4	0.874	Contact Map
4wisA	2	0.75	2.2	0.876	Contact Map
2m3eA	1	0.8393	2.2	0.877	Contact Map
2lzpA	1	0.5179	2.1	0.878	Contact Map
3rqwA	4	0.9643	2	0.879	Contact Map
3w4tA	1	0.6429	1.9	0.881	Contact Map
3weoA	1	0	1.9	0.881	Contact Map
3orgA	2	0.8214	1.8	0.882	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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