DUF3293 - PFAM28P - GREMLIN Contacts

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DUF3293 - Protein of unknown function (DUF3293)

PFAM:	PF11697	Sequences: ITAWNPRSEPLSDAENAARNARLEAELRALGLRFLPGEGRDPDGSWPEPSFLVLGISREEAIALGRRFGQNAI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	73 (73)
Sequences:	6399 (5145)
Seq/√Len:	602.2
META:	0.932

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_E	67_R	2.983	1.00
26_E	68_F	2.517	1.00
11_L	19_R	2.153	1.00
4_W	20_N	2.140	1.00
20_N	51_F	2.135	1.00
4_W	49_P	1.971	1.00
24_E	51_F	1.955	1.00
12_S	15_E	1.898	1.00
56_I	61_A	1.803	1.00
57_S	60_E	1.803	1.00
32_L	53_V	1.662	1.00
7_R	69_G	1.653	1.00
13_D	17_A	1.648	1.00
24_E	28_R	1.630	1.00
35_L	54_L	1.607	1.00
8_S	71_N	1.607	1.00
37_G	50_S	1.569	1.00
24_E	36_P	1.544	1.00
27_L	51_F	1.531	1.00
3_A	20_N	1.487	1.00
58_R	62_I	1.466	1.00
11_L	15_E	1.436	1.00
41_D	45_S	1.335	1.00
30_L	60_E	1.314	1.00
26_E	30_L	1.291	1.00
65_G	73_I	1.290	1.00
37_G	52_L	1.278	1.00
7_R	71_N	1.264	1.00
24_E	34_F	1.240	1.00
19_R	69_G	1.207	1.00
19_R	22_R	1.202	1.00
28_R	34_F	1.188	1.00
20_N	24_E	1.159	1.00
40_R	44_G	1.137	1.00
2_T	20_N	1.130	1.00
27_L	53_V	1.115	1.00
3_A	23_L	1.115	1.00
20_N	36_P	1.098	1.00
34_F	51_F	1.079	1.00
20_N	49_P	1.067	1.00
8_S	46_W	0.979	1.00
38_E	47_P	0.966	1.00
62_I	65_G	0.963	1.00
41_D	44_G	0.945	1.00
62_I	66_R	0.936	1.00
22_R	26_E	0.923	1.00
30_L	64_L	0.908	1.00
25_A	29_A	0.896	1.00
39_G	50_S	0.856	1.00
32_L	56_I	0.851	1.00
38_E	49_P	0.850	1.00
31_G	34_F	0.841	1.00
53_V	56_I	0.834	1.00
60_E	63_A	0.833	1.00
17_A	49_P	0.831	1.00
18_A	22_R	0.818	1.00
27_L	64_L	0.818	1.00
32_L	60_E	0.786	1.00
21_A	24_E	0.783	1.00
40_R	47_P	0.776	1.00
34_F	54_L	0.758	1.00
20_N	50_S	0.754	1.00
15_E	19_R	0.753	1.00
4_W	17_A	0.750	1.00
63_A	67_R	0.745	1.00
35_L	52_L	0.742	1.00
26_E	29_A	0.732	1.00
46_W	72_A	0.729	1.00
57_S	61_A	0.726	1.00
21_A	25_A	0.716	1.00
56_I	60_E	0.705	1.00
23_L	68_F	0.704	1.00
27_L	34_F	0.673	1.00
22_R	67_R	0.663	1.00
23_L	64_L	0.661	1.00
2_T	50_S	0.657	1.00
1_I	53_V	0.653	1.00
4_W	13_D	0.652	1.00
5_N	16_N	0.646	1.00
46_W	52_L	0.643	1.00
62_I	73_I	0.637	1.00
61_A	73_I	0.635	1.00
15_E	18_A	0.622	1.00
22_R	25_A	0.615	1.00
46_W	71_N	0.613	1.00
23_L	65_G	0.605	1.00
22_R	68_F	0.599	1.00
18_A	21_A	0.592	1.00
61_A	65_G	0.586	1.00
44_G	47_P	0.585	1.00
8_S	11_L	0.577	1.00
41_D	46_W	0.572	1.00
14_A	18_A	0.560	1.00
65_G	72_A	0.558	1.00
38_E	50_S	0.555	0.99
31_G	53_V	0.555	0.99
27_L	32_L	0.552	0.99
17_A	21_A	0.551	0.99
39_G	47_P	0.550	0.99
7_R	11_L	0.546	0.99
41_D	47_P	0.544	0.99
59_E	63_A	0.536	0.99
64_L	68_F	0.535	0.99
36_P	49_P	0.527	0.99
6_P	11_L	0.526	0.99
10_P	44_G	0.508	0.99
37_G	55_G	0.501	0.99
56_I	64_L	0.500	0.99
30_L	67_R	0.500	0.99
42_P	46_W	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
2qlcA	1	0.7123	61	0.809	Contact Map
1g03A	1	0.6438	20.6	0.854	Contact Map
4ph2A	1	0.5616	14	0.865	Contact Map
3d64A	4	0.8493	9.5	0.875	Contact Map
3tgoC	2	0	9.3	0.875	Contact Map
3l21A	5	0.9315	6.7	0.883	Contact Map
4bjuA	1	0.726	6.4	0.884	Contact Map
4oe7A	3	0.9315	6.1	0.885	Contact Map
3cprA	3	0.9315	6	0.885	Contact Map
4dppA	3	0.9315	5.9	0.886	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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