DUF2839 - PFAM28P - GREMLIN Contacts

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DUF2839 - Protein of unknown function (DUF2839)

PFAM:	PF10999	Sequences: MGEAKRRKQGLGPRYGKEPRILPWLPITKNQAEQFVKWTTRGAWIGIGLLVVLWVTVRFIGPAFGWW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	67 (67)
Sequences:	561 (272)
Seq/√Len:	33.2
META:	0.774

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_T	60_I	2.676	1.00
32_A	36_V	2.406	0.99
53_L	57_V	2.389	0.99
12_G	15_Y	2.101	0.98
45_I	48_G	2.067	0.98
40_T	43_A	2.027	0.98
28_T	31_Q	1.982	0.98
14_R	17_K	1.836	0.96
12_G	16_G	1.786	0.96
18_E	30_N	1.698	0.94
43_A	46_G	1.602	0.92
19_P	30_N	1.568	0.92
36_V	39_T	1.561	0.91
19_P	64_F	1.496	0.90
27_I	32_A	1.470	0.89
48_G	52_V	1.435	0.87
20_R	24_W	1.425	0.87
39_T	42_G	1.416	0.87
46_G	57_V	1.403	0.86
10_G	13_P	1.392	0.86
36_V	43_A	1.360	0.84
21_I	31_Q	1.314	0.82
20_R	63_A	1.269	0.80
26_P	31_Q	1.261	0.80
22_L	25_L	1.243	0.79
27_I	31_Q	1.215	0.77
21_I	26_P	1.201	0.76
36_V	40_T	1.195	0.76
5_K	37_K	1.184	0.75
35_F	42_G	1.179	0.75
55_V	60_I	1.139	0.72
8_K	12_G	1.117	0.71
35_F	39_T	1.102	0.70
62_P	65_G	1.039	0.65
20_R	53_L	1.037	0.65
55_V	59_F	1.004	0.62
45_I	52_V	1.002	0.62
49_L	52_V	0.986	0.61
44_W	47_I	0.975	0.60
10_G	14_R	0.963	0.59
20_R	28_T	0.948	0.58
22_L	27_I	0.942	0.57
46_G	50_L	0.923	0.56
11_L	15_Y	0.920	0.56
1_M	4_A	0.913	0.55
7_R	13_P	0.907	0.54
2_G	5_K	0.906	0.54
36_V	51_V	0.896	0.54
29_K	32_A	0.853	0.50
5_K	64_F	0.851	0.50
53_L	59_F	0.831	0.48
5_K	9_Q	0.810	0.46
41_R	45_I	0.809	0.46
19_P	25_L	0.807	0.46
1_M	5_K	0.798	0.45
61_G	67_W	0.796	0.45
19_P	29_K	0.780	0.44
37_K	49_L	0.777	0.44
4_A	55_V	0.760	0.42
49_L	56_T	0.759	0.42
17_K	53_L	0.754	0.42
35_F	38_W	0.753	0.42
32_A	40_T	0.750	0.41
11_L	17_K	0.739	0.41
57_V	64_F	0.725	0.39
60_I	64_F	0.723	0.39
37_K	41_R	0.710	0.38
49_L	53_L	0.698	0.37
8_K	49_L	0.692	0.37
30_N	66_W	0.679	0.36
3_E	64_F	0.678	0.36
21_I	27_I	0.674	0.35
2_G	6_R	0.674	0.35
38_W	42_G	0.668	0.35
11_L	14_R	0.650	0.34
8_K	14_R	0.636	0.33
1_M	6_R	0.609	0.31
34_Q	37_K	0.603	0.30
54_W	58_R	0.600	0.30
9_Q	12_G	0.584	0.29
23_P	27_I	0.581	0.29
20_R	26_P	0.580	0.29
38_W	41_R	0.578	0.28
35_F	43_A	0.572	0.28
20_R	31_Q	0.572	0.28
5_K	8_K	0.569	0.28
13_P	16_G	0.568	0.28
8_K	15_Y	0.564	0.28
5_K	32_A	0.556	0.27
63_A	66_W	0.540	0.26
32_A	43_A	0.539	0.26
43_A	47_I	0.537	0.26
62_P	67_W	0.534	0.26
39_T	45_I	0.533	0.26
28_T	63_A	0.527	0.25
34_Q	55_V	0.519	0.25
3_E	6_R	0.515	0.24
39_T	50_L	0.509	0.24
43_A	50_L	0.503	0.24
60_I	66_W	0.500	0.23

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
2mmuA	1	0.4179	58.8	0.878	Contact Map
3prhA	2	0	27.8	0.9	Contact Map
2axcA	1	0.3433	3.9	0.932	Contact Map
2jlnA	1	0.7761	3.5	0.934	Contact Map
1n0uA	1	0.3582	3	0.936	Contact Map
2k4fA	1	0.6269	2.8	0.937	Contact Map
2h88C	2	0.9851	2.8	0.937	Contact Map
1zoyC	1	0.9701	2.8	0.937	Contact Map
4w224	1	0.3582	2.5	0.939	Contact Map
4cr2W	1	0	2.4	0.939	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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