DUF2281 - PFAM28P - GREMLIN Contacts

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DUF2281 - Protein of unknown function (DUF2281)

PFAM:	PF10047	Sequences: TEEQLEEKIEELPPELQKEVLDFVEFLLEKRKKKKKKKKRLFGSWKGALKMSDDFDTPLELQKKYM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	66 (63)
Sequences:	3955 (2938)
Seq/√Len:	370.2
META:	0.944

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_K	25_E	3.489	1.00
8_K	24_V	2.661	1.00
8_K	28_L	2.545	1.00
20_V	24_V	2.509	1.00
6_E	10_E	2.234	1.00
16_L	31_R	2.104	1.00
22_D	26_F	2.062	1.00
19_E	30_K	1.840	1.00
59_L	63_K	1.796	1.00
43_G	46_K	1.768	1.00
26_F	30_K	1.681	1.00
11_E	28_L	1.679	1.00
13_P	16_L	1.593	1.00
52_S	55_F	1.502	1.00
23_F	26_F	1.420	1.00
18_K	21_L	1.360	1.00
5_L	9_I	1.358	1.00
14_P	17_Q	1.334	1.00
20_V	27_L	1.322	1.00
40_R	44_S	1.297	1.00
45_W	48_A	1.233	1.00
12_L	24_V	1.230	1.00
19_E	22_D	1.222	1.00
41_L	45_W	1.189	1.00
18_K	22_D	1.173	1.00
8_K	21_L	1.113	1.00
19_E	26_F	1.103	1.00
9_I	17_Q	1.080	1.00
13_P	31_R	1.069	1.00
26_F	29_E	1.011	1.00
45_W	49_L	0.991	1.00
54_D	57_T	0.988	1.00
62_Q	65_Y	0.966	1.00
12_L	16_L	0.947	1.00
51_M	55_F	0.944	1.00
7_E	10_E	0.923	1.00
16_L	23_F	0.920	1.00
4_Q	7_E	0.919	1.00
6_E	17_Q	0.904	1.00
19_E	23_F	0.875	1.00
51_M	54_D	0.864	1.00
22_D	30_K	0.851	1.00
44_S	48_A	0.844	1.00
40_R	43_G	0.832	1.00
55_F	58_P	0.820	1.00
57_T	61_L	0.808	1.00
17_Q	21_L	0.805	1.00
4_Q	25_E	0.804	1.00
9_I	21_L	0.804	1.00
9_I	24_V	0.799	1.00
43_G	48_A	0.794	1.00
41_L	44_S	0.789	1.00
42_F	45_W	0.771	1.00
21_L	25_E	0.768	1.00
25_E	28_L	0.759	1.00
4_Q	21_L	0.755	1.00
15_E	31_R	0.736	1.00
25_E	30_K	0.725	1.00
21_L	24_V	0.715	1.00
53_D	56_D	0.696	0.99
3_E	6_E	0.685	0.99
16_L	19_E	0.684	0.99
52_S	56_D	0.677	0.99
12_L	17_Q	0.667	0.99
50_K	53_D	0.666	0.99
57_T	62_Q	0.666	0.99
4_Q	8_K	0.664	0.99
38_K	44_S	0.653	0.99
39_K	45_W	0.640	0.99
14_P	18_K	0.632	0.99
23_F	31_R	0.623	0.99
6_E	9_I	0.613	0.99
56_D	59_L	0.607	0.98
56_D	62_Q	0.601	0.98
52_S	59_L	0.594	0.98
61_L	65_Y	0.590	0.98
3_E	7_E	0.585	0.98
3_E	11_E	0.585	0.98
58_P	61_L	0.564	0.97
52_S	63_K	0.562	0.97
54_D	58_P	0.552	0.97
60_E	63_K	0.543	0.97
36_K	40_R	0.542	0.97
42_F	48_A	0.533	0.96
32_K	35_K	0.532	0.96
3_E	10_E	0.529	0.96
40_R	45_W	0.529	0.96
59_L	62_Q	0.528	0.96
5_L	21_L	0.521	0.96
8_K	11_E	0.521	0.96
58_P	62_Q	0.516	0.96
3_E	21_L	0.506	0.95
5_L	24_V	0.501	0.95
52_S	57_T	0.500	0.95

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
4jcyA	2	0.3485	48.5	0.778	Contact Map
3r1fA	2	0.5152	39.4	0.79	Contact Map
4ndwA	2	0.5152	39.1	0.79	Contact Map
3op9A	4	0.5	23.6	0.812	Contact Map
3qwgA	2	0	16	0.827	Contact Map
1wixA	1	0.5455	15.6	0.827	Contact Map
3mavA	2	0.4394	14.6	0.83	Contact Map
2ebyA	2	0.5	14.2	0.83	Contact Map
4o8bA	2	0.4848	13.9	0.831	Contact Map
3ivpA	2	0.5303	13.8	0.831	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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