Ytca - PFAM28P - GREMLIN Contacts

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Ytca - Uncharacterised protein family

PFAM:	PF17090	Sequences: APSFDILGSFFPAWLLCLVIGIVLTVVARWLLVRLGLELGPPPLVYPSLAALFTFALWLLFF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	62 (62)
Sequences:	3128 (1624)
Seq/√Len:	206.2
META:	0.946

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_L	53_F	5.449	1.00
28_A	53_F	3.011	1.00
51_A	55_F	2.935	1.00
40_G	43_P	2.269	1.00
43_P	47_P	2.237	1.00
29_R	33_V	2.171	1.00
20_I	57_L	1.902	1.00
7_L	10_F	1.848	1.00
3_S	7_L	1.739	1.00
18_L	40_G	1.617	1.00
5_D	13_A	1.526	1.00
40_G	45_V	1.503	1.00
47_P	50_A	1.441	1.00
41_P	45_V	1.419	1.00
33_V	36_G	1.352	1.00
16_L	20_I	1.349	1.00
25_T	50_A	1.285	1.00
15_L	42_P	1.277	1.00
6_I	11_F	1.277	1.00
31_L	35_L	1.218	1.00
4_F	16_L	1.201	1.00
21_G	57_L	1.181	1.00
52_L	56_A	1.151	1.00
46_Y	50_A	1.099	1.00
42_P	45_V	1.050	1.00
13_A	55_F	1.024	1.00
9_S	54_T	1.008	1.00
56_A	60_L	0.985	1.00
18_L	50_A	0.982	1.00
4_F	62_F	0.974	1.00
23_V	27_V	0.971	1.00
26_V	29_R	0.927	0.99
22_I	50_A	0.903	0.99
39_L	43_P	0.887	0.99
6_I	16_L	0.887	0.99
36_G	62_F	0.885	0.99
1_A	4_F	0.884	0.99
37_L	45_V	0.883	0.99
30_W	34_R	0.880	0.99
17_C	55_F	0.854	0.99
5_D	21_G	0.851	0.99
15_L	19_V	0.844	0.99
9_S	15_L	0.840	0.99
39_L	42_P	0.830	0.99
52_L	55_F	0.829	0.99
26_V	30_W	0.822	0.98
32_L	35_L	0.820	0.98
21_G	25_T	0.818	0.98
27_V	31_L	0.809	0.98
20_I	24_L	0.803	0.98
1_A	32_L	0.789	0.98
21_G	50_A	0.745	0.97
49_L	53_F	0.743	0.97
28_A	49_L	0.743	0.97
47_P	51_A	0.727	0.97
55_F	59_L	0.720	0.96
7_L	11_F	0.719	0.96
57_L	60_L	0.710	0.96
53_F	61_F	0.701	0.96
19_V	23_V	0.672	0.95
29_R	46_Y	0.670	0.95
23_V	30_W	0.669	0.95
32_L	49_L	0.666	0.95
17_C	61_F	0.659	0.94
38_E	43_P	0.639	0.93
41_P	44_L	0.619	0.92
7_L	15_L	0.611	0.92
15_L	51_A	0.605	0.91
10_F	16_L	0.597	0.91
23_V	58_W	0.592	0.90
15_L	40_G	0.592	0.90
34_R	51_A	0.590	0.90
25_T	49_L	0.586	0.90
1_A	10_F	0.585	0.90
5_D	55_F	0.578	0.89
1_A	17_C	0.577	0.89
22_I	58_W	0.575	0.89
18_L	57_L	0.568	0.88
3_S	10_F	0.565	0.88
46_Y	49_L	0.560	0.88
28_A	46_Y	0.559	0.88
27_V	30_W	0.554	0.87
13_A	16_L	0.550	0.87
19_V	57_L	0.548	0.87
57_L	61_F	0.547	0.86
7_L	22_I	0.544	0.86
55_F	62_F	0.536	0.85
48_S	51_A	0.534	0.85
5_D	9_S	0.519	0.84
44_L	59_L	0.512	0.83
15_L	47_P	0.512	0.83
13_A	57_L	0.504	0.82
19_V	38_E	0.500	0.81

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
4qinA	2	1	3.7	0.891	Contact Map
4jkvA	2	1	3.5	0.892	Contact Map
3ixzB	1	0.4516	2.8	0.897	Contact Map
3wguB	1	0.7742	2.8	0.898	Contact Map
4ezcA	3	0.8548	2.5	0.9	Contact Map
4nv5A	1	0.9677	2.2	0.902	Contact Map
3dh4A	3	1	2	0.905	Contact Map
3hd6A	3	0.9677	1.7	0.909	Contact Map
3o7qA	1	0.5484	1.7	0.909	Contact Map
4hfiA	3	1	1.5	0.911	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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