DUF2842 - PFAM28P - GREMLIN Contacts

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DUF2842 - Protein of unknown function (DUF2842)

PFAM:	PF11003	Sequences: RKLIGTVALLVLLPVYALLAMALAQALLGRAPWLVQLLYYVVAGLAWVLPAKPLIRWMERP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	61 (60)
Sequences:	6156 (3554)
Seq/√Len:	458.8
META:	0.925

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_Y	43_A	3.031	1.00
5_G	58_M	2.093	1.00
20_A	43_A	2.030	1.00
4_I	7_V	1.941	1.00
33_W	37_L	1.907	1.00
18_L	21_M	1.867	1.00
3_L	6_T	1.688	1.00
22_A	25_Q	1.683	1.00
52_K	56_R	1.680	1.00
21_M	25_Q	1.646	1.00
18_L	22_A	1.618	1.00
9_L	51_A	1.612	1.00
7_V	11_V	1.612	1.00
22_A	26_A	1.524	1.00
24_A	39_Y	1.461	1.00
12_L	51_A	1.431	1.00
53_P	56_R	1.356	1.00
32_P	35_V	1.300	1.00
30_R	36_Q	1.295	1.00
16_Y	46_A	1.295	1.00
2_K	59_E	1.282	1.00
52_K	55_I	1.276	1.00
27_L	30_R	1.267	1.00
17_A	21_M	1.257	1.00
23_L	26_A	1.256	1.00
12_L	16_Y	1.196	1.00
3_L	7_V	1.180	1.00
8_A	54_L	1.179	1.00
37_L	41_V	1.081	1.00
8_A	12_L	1.053	1.00
23_L	27_L	1.048	1.00
33_W	36_Q	1.043	1.00
42_V	46_A	1.037	1.00
55_I	59_E	1.036	1.00
31_A	36_Q	1.019	1.00
49_L	52_K	1.012	1.00
19_L	22_A	1.012	1.00
45_L	48_V	0.966	1.00
34_L	38_L	0.947	1.00
51_A	55_I	0.944	1.00
31_A	35_V	0.936	1.00
38_L	42_V	0.936	1.00
24_A	40_Y	0.933	1.00
56_R	60_R	0.921	1.00
15_V	18_L	0.883	1.00
30_R	33_W	0.881	1.00
26_A	31_A	0.866	1.00
38_L	41_V	0.858	1.00
10_L	14_P	0.812	1.00
48_V	52_K	0.803	1.00
49_L	53_P	0.772	1.00
48_V	53_P	0.751	1.00
20_A	39_Y	0.749	1.00
26_A	29_G	0.744	1.00
31_A	39_Y	0.741	1.00
16_Y	19_L	0.738	1.00
27_L	31_A	0.732	1.00
8_A	51_A	0.712	1.00
14_P	17_A	0.701	1.00
4_I	8_A	0.694	1.00
28_L	36_Q	0.687	1.00
36_Q	40_Y	0.673	1.00
45_L	49_L	0.665	1.00
13_L	48_V	0.663	1.00
16_Y	20_A	0.659	1.00
35_V	38_L	0.657	1.00
2_K	5_G	0.653	1.00
44_G	48_V	0.653	1.00
48_V	55_I	0.652	1.00
51_A	54_L	0.638	0.99
28_L	45_L	0.636	0.99
13_L	17_A	0.635	0.99
14_P	18_L	0.633	0.99
21_M	24_A	0.603	0.99
25_Q	40_Y	0.594	0.99
2_K	58_M	0.592	0.99
19_L	23_L	0.571	0.99
20_A	24_A	0.549	0.99
2_K	6_T	0.548	0.98
51_A	59_E	0.544	0.98
21_M	29_G	0.538	0.98
45_L	52_K	0.533	0.98
54_L	58_M	0.530	0.98
6_T	10_L	0.525	0.98
56_R	59_E	0.523	0.98
46_A	49_L	0.520	0.98
57_W	60_R	0.504	0.97
11_V	14_P	0.503	0.97
52_K	59_E	0.500	0.97
9_L	12_L	0.500	0.97

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
2l6wA	2	0.5902	2.6	0.885	Contact Map
2kogA	1	0.3443	2.1	0.89	Contact Map
1orqC	4	0.5246	1.7	0.895	Contact Map
2w0cT	1	0.3443	1.7	0.895	Contact Map
1jb0B	1	0.8689	1.5	0.899	Contact Map
4cadC	1	0.918	1.3	0.903	Contact Map
4px7A	1	0.9016	1.2	0.904	Contact Map
3ldcA	3	0.459	1.2	0.905	Contact Map
3hd7A	1	0.3934	1.1	0.908	Contact Map
4wl1A	3	0	1	0.908	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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