DUF2809 - PFAM28P - GREMLIN Contacts

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DUF2809 - Protein of unknown function (DUF2809)

PFAM:	PF10990	Sequences: VHPGFIRKYLGDALWAIMVYLLVRLLFPRASLLRIALAALLFAFAVEFSQLYHAPWLLGLRATTLGRLVLGSGFSWSDLLAYAVGI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	86 (83)
Sequences:	7033 (5412)
Seq/√Len:	594.0
META:	0.878

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
40_L	44_F	2.765	1.00
67_R	72_S	2.689	1.00
53_H	58_L	2.547	1.00
24_R	35_I	2.544	1.00
44_F	83_A	2.145	1.00
30_A	34_R	2.080	1.00
50_Q	78_D	1.988	1.00
16_A	43_A	1.896	1.00
63_T	66_G	1.870	1.00
64_T	67_R	1.755	1.00
44_F	79_L	1.742	1.00
40_L	83_A	1.730	1.00
7_R	10_L	1.729	1.00
13_A	84_V	1.647	1.00
19_V	39_A	1.594	1.00
4_G	8_K	1.569	1.00
64_T	68_L	1.523	1.00
53_H	56_W	1.505	1.00
16_A	86_I	1.493	1.00
56_W	61_R	1.485	1.00
54_A	58_L	1.464	1.00
45_A	49_S	1.453	1.00
22_L	26_L	1.437	1.00
23_V	42_F	1.424	1.00
48_F	52_Y	1.420	1.00
30_A	35_I	1.415	1.00
10_L	13_A	1.309	1.00
13_A	81_A	1.289	1.00
29_R	34_R	1.256	1.00
52_Y	57_L	1.228	1.00
15_W	19_V	1.220	1.00
31_S	34_R	1.215	1.00
15_W	43_A	1.211	1.00
30_A	33_L	1.203	1.00
9_Y	81_A	1.194	1.00
18_M	22_L	1.191	1.00
27_F	30_A	1.171	1.00
54_A	57_L	1.154	1.00
72_S	75_S	1.149	1.00
76_W	79_L	1.147	1.00
77_S	81_A	1.142	1.00
19_V	42_F	1.097	1.00
60_L	66_G	1.090	1.00
9_Y	77_S	1.086	1.00
76_W	80_L	1.051	1.00
20_Y	32_L	1.029	1.00
17_I	21_L	1.029	1.00
19_V	43_A	1.015	1.00
23_V	35_I	0.988	1.00
36_A	86_I	0.984	1.00
57_L	61_R	0.975	1.00
49_S	58_L	0.974	1.00
49_S	54_A	0.946	1.00
65_L	69_V	0.940	1.00
49_S	52_Y	0.897	1.00
41_L	45_A	0.895	1.00
5_F	10_L	0.884	1.00
44_F	48_F	0.872	1.00
42_F	46_V	0.861	1.00
59_G	63_T	0.850	1.00
55_P	70_L	0.849	1.00
30_A	38_A	0.849	1.00
43_A	46_V	0.842	1.00
63_T	68_L	0.833	1.00
75_S	79_L	0.827	1.00
53_H	57_L	0.814	1.00
77_S	80_L	0.798	1.00
32_L	35_I	0.794	1.00
38_A	42_F	0.758	1.00
20_Y	24_R	0.755	1.00
15_W	46_V	0.754	1.00
48_F	51_L	0.749	1.00
22_L	25_L	0.720	1.00
40_L	86_I	0.689	1.00
27_F	35_I	0.686	1.00
32_L	36_A	0.682	1.00
20_Y	36_A	0.679	1.00
19_V	46_V	0.670	1.00
8_K	12_D	0.662	1.00
79_L	83_A	0.659	1.00
6_I	10_L	0.654	1.00
52_Y	56_W	0.654	1.00
55_P	59_G	0.654	1.00
8_K	75_S	0.648	1.00
62_A	67_R	0.643	1.00
57_L	60_L	0.643	1.00
54_A	70_L	0.640	1.00
39_A	86_I	0.640	1.00
24_R	28_P	0.631	1.00
23_V	38_A	0.623	1.00
37_L	41_L	0.622	1.00
40_L	79_L	0.617	1.00
27_F	34_R	0.612	1.00
24_R	32_L	0.610	1.00
15_W	49_S	0.609	1.00
24_R	30_A	0.604	1.00
38_A	41_L	0.600	1.00
29_R	33_L	0.600	1.00
57_L	70_L	0.599	1.00
16_A	39_A	0.596	1.00
53_H	72_S	0.585	1.00
24_R	27_F	0.581	1.00
33_L	36_A	0.578	1.00
60_L	63_T	0.575	1.00
81_A	85_G	0.563	1.00
81_A	84_V	0.561	1.00
61_R	66_G	0.559	0.99
65_L	68_L	0.553	0.99
25_L	29_R	0.552	0.99
18_M	21_L	0.546	0.99
24_R	31_S	0.544	0.99
12_D	46_V	0.543	0.99
14_L	17_I	0.541	0.99
67_R	73_G	0.537	0.99
73_G	77_S	0.536	0.99
10_L	81_A	0.535	0.99
48_F	79_L	0.531	0.99
52_Y	58_L	0.523	0.99
36_A	39_A	0.519	0.99
75_S	81_A	0.507	0.99
50_Q	73_G	0.504	0.99
50_Q	65_L	0.503	0.99
47_E	50_Q	0.502	0.99
14_L	18_M	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
4m5bA	1	0.9884	2.1	0.924	Contact Map
2jm6A	1	0.314	1.9	0.926	Contact Map
2gqrA	2	0.3372	1.4	0.931	Contact Map
1sv0C	1	0.3256	1.4	0.931	Contact Map
1wf6A	1	0.3372	1.4	0.932	Contact Map
3j9pD	4	0.686	1.4	0.932	Contact Map
4k0jA	3	0.7674	1.1	0.935	Contact Map
4p6vB	1	0.8953	1	0.937	Contact Map
3rceA	1	0.9302	1	0.937	Contact Map
2mnsA	1	0.1163	1	0.938	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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