DUF2812 - PFAM28P - GREMLIN Contacts

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DUF2812 - Protein of unknown function (DUF2812)

PFAM:	PF11193	Sequences: DYEKEEKWLNEMAAKGWHLKKVGFFGYTFEKGEPGEYIYRLDYLPKKSKEESEEYLELFEDAGWEYVGSSGGWQYFRKEADDGPPEIYTDPESKIEKYKRILRFLLILFL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	110 (103)
Sequences:	3538 (2792)
Seq/√Len:	275.1
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
20_K	30_E	4.305	1.00
18_H	32_G	3.831	1.00
65_E	77_R	2.714	1.00
14_A	36_E	2.343	1.00
6_E	40_R	2.219	1.00
35_G	79_E	2.180	1.00
8_W	29_F	2.150	1.00
13_A	18_H	2.148	1.00
37_Y	77_R	2.137	1.00
12_M	15_K	1.953	1.00
17_W	31_K	1.936	1.00
38_I	80_A	1.909	1.00
59_F	76_F	1.828	1.00
5_E	27_Y	1.760	1.00
42_D	55_Y	1.758	1.00
10_N	36_E	1.750	1.00
66_Y	74_Q	1.740	1.00
59_F	87_I	1.693	1.00
13_A	37_Y	1.692	1.00
21_K	28_T	1.572	1.00
57_E	61_D	1.470	1.00
5_E	75_Y	1.469	1.00
36_E	79_E	1.425	1.00
88_Y	93_S	1.403	1.00
69_S	74_Q	1.367	1.00
66_Y	69_S	1.357	1.00
60_E	65_E	1.349	1.00
42_D	88_Y	1.336	1.00
12_M	29_F	1.321	1.00
59_F	64_W	1.297	1.00
51_E	54_E	1.289	1.00
40_R	86_E	1.272	1.00
56_L	66_Y	1.257	1.00
13_A	32_G	1.240	1.00
19_L	75_Y	1.230	1.00
11_E	15_K	1.227	1.00
18_H	35_G	1.216	1.00
8_W	12_M	1.197	1.00
78_K	82_D	1.194	1.00
56_L	76_F	1.191	1.00
19_L	22_V	1.153	1.00
37_Y	79_E	1.146	1.00
18_H	77_R	1.142	1.00
57_E	60_E	1.141	1.00
18_H	39_Y	1.116	1.00
20_K	28_T	1.114	1.00
7_K	11_E	1.111	1.00
10_N	38_I	1.091	1.00
39_Y	67_V	1.075	1.00
39_Y	77_R	1.061	1.00
99_K	103_R	1.052	1.00
6_E	10_N	1.050	1.00
78_K	83_G	1.042	1.00
11_E	14_A	1.026	1.00
90_D	93_S	1.026	1.00
18_H	30_E	1.011	1.00
10_N	14_A	1.009	1.00
36_E	80_A	0.986	1.00
13_A	39_Y	0.983	1.00
22_V	70_S	0.971	1.00
102_L	105_L	0.969	1.00
9_L	75_Y	0.947	1.00
58_L	62_A	0.941	1.00
52_S	69_S	0.940	1.00
67_V	77_R	0.936	1.00
32_G	39_Y	0.924	1.00
38_I	78_K	0.907	1.00
52_S	56_L	0.900	1.00
91_P	94_K	0.896	1.00
46_K	52_S	0.889	1.00
59_F	62_A	0.880	1.00
97_K	101_I	0.879	1.00
102_L	106_L	0.858	1.00
38_I	83_G	0.857	1.00
22_V	75_Y	0.837	1.00
18_H	37_Y	0.836	1.00
9_L	41_L	0.830	1.00
3_E	6_E	0.826	0.99
23_G	28_T	0.819	0.99
55_Y	59_F	0.807	0.99
66_Y	76_F	0.807	0.99
41_L	75_Y	0.788	0.99
96_E	103_R	0.786	0.99
89_T	93_S	0.785	0.99
19_L	68_G	0.780	0.99
58_L	61_D	0.778	0.99
55_Y	58_L	0.776	0.99
5_E	9_L	0.770	0.99
56_L	60_E	0.758	0.99
54_E	57_E	0.734	0.99
58_L	89_T	0.726	0.99
42_D	100_R	0.702	0.98
8_W	27_Y	0.696	0.98
40_R	87_I	0.693	0.98
32_G	35_G	0.685	0.98
13_A	35_G	0.682	0.98
9_L	27_Y	0.681	0.98
45_P	100_R	0.673	0.98
13_A	34_P	0.670	0.98
56_L	59_F	0.669	0.98
55_Y	89_T	0.669	0.98
38_I	85_P	0.667	0.98
7_K	14_A	0.665	0.98
103_R	106_L	0.663	0.98
49_K	52_S	0.659	0.98
43_Y	72_G	0.658	0.97
45_P	96_E	0.653	0.97
94_K	98_Y	0.647	0.97
42_D	97_K	0.646	0.97
64_W	76_F	0.640	0.97
54_E	58_L	0.626	0.97
53_E	57_E	0.618	0.96
41_L	73_W	0.612	0.96
91_P	95_I	0.611	0.96
65_E	79_E	0.599	0.96
64_W	74_Q	0.598	0.96
96_E	99_K	0.590	0.95
64_W	85_P	0.586	0.95
86_E	94_K	0.585	0.95
21_K	92_E	0.582	0.95
12_M	17_W	0.577	0.95
79_E	82_D	0.571	0.94
45_P	52_S	0.570	0.94
35_G	80_A	0.569	0.94
53_E	56_L	0.566	0.94
31_K	34_P	0.562	0.94
99_K	102_L	0.559	0.94
52_S	66_Y	0.559	0.94
70_S	105_L	0.556	0.94
24_F	71_G	0.547	0.93
44_L	74_Q	0.544	0.93
98_Y	102_L	0.543	0.93
44_L	55_Y	0.539	0.92
33_E	53_E	0.535	0.92
80_A	83_G	0.533	0.92
59_F	93_S	0.532	0.92
10_N	34_P	0.532	0.92
32_G	36_E	0.530	0.92
10_N	64_W	0.525	0.91
17_W	54_E	0.517	0.91
10_N	37_Y	0.514	0.91
94_K	97_K	0.514	0.91
95_I	98_Y	0.513	0.91
48_S	71_G	0.512	0.90
20_K	26_G	0.510	0.90
20_K	24_F	0.509	0.90
73_W	77_R	0.508	0.90
95_I	99_K	0.508	0.90
55_Y	62_A	0.506	0.90
22_V	27_Y	0.506	0.90
17_W	98_Y	0.506	0.90
48_S	96_E	0.504	0.90
27_Y	42_D	0.501	0.90
18_H	33_E	0.500	0.89

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
4p78C	1	0.5545	23.4	0.877	Contact Map
4c26A	1	0.5909	22.1	0.878	Contact Map
3tc3A	1	0.8636	10.8	0.894	Contact Map
3lxuX	2	0.6182	10.1	0.896	Contact Map
1whzA	1	0.5909	9	0.898	Contact Map
2zfuA	1	0.5364	8.4	0.9	Contact Map
2j6vA	1	0.9545	8.1	0.9	Contact Map
4nnbA	1	0.5364	7.7	0.901	Contact Map
4khoA	1	0.4545	6.8	0.904	Contact Map
4m1bA	1	0.2636	6.7	0.904	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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