DUF1843 - PFAM28P - GREMLIN Contacts

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DUF1843 - Domain of unknown function (DUF1843)

PFAM:	PF08898	Sequences: PLYGVAIQEAIASGDLAEMKALAAQAEKHLAEHGDVRAALEALKAEIAKLEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	52 (51)
Sequences:	635 (435)
Seq/√Len:	60.9
META:	0.879

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
13_S	18_E	3.442	1.00
23_A	40_L	2.795	1.00
27_E	44_K	2.268	1.00
2_L	6_A	2.191	1.00
13_S	22_L	1.789	1.00
29_H	33_H	1.750	0.99
29_H	36_V	1.729	0.99
7_I	11_I	1.717	0.99
33_H	36_V	1.651	0.99
18_E	21_A	1.520	0.98
15_D	18_E	1.517	0.98
42_A	45_A	1.496	0.98
34_G	37_R	1.466	0.98
2_L	29_H	1.395	0.97
2_L	25_Q	1.259	0.95
28_K	32_E	1.213	0.94
6_A	10_A	1.208	0.94
7_I	19_M	1.198	0.93
2_L	26_A	1.195	0.93
6_A	22_L	1.166	0.92
16_L	47_I	1.138	0.91
16_L	20_K	1.133	0.91
35_D	38_A	1.133	0.91
2_L	10_A	1.132	0.91
22_L	25_Q	1.111	0.90
30_L	40_L	1.090	0.89
22_L	26_A	1.088	0.89
8_Q	39_A	1.071	0.89
41_E	45_A	1.054	0.88
33_H	37_R	1.039	0.87
19_M	23_A	1.028	0.86
9_E	18_E	0.943	0.81
20_K	23_A	0.927	0.80
28_K	31_A	0.890	0.77
21_A	25_Q	0.873	0.76
6_A	9_E	0.866	0.75
35_D	41_E	0.864	0.75
20_K	24_A	0.857	0.75
10_A	18_E	0.846	0.74
27_E	31_A	0.803	0.70
11_I	45_A	0.780	0.68
45_A	48_A	0.762	0.66
8_Q	46_E	0.754	0.65
24_A	28_K	0.730	0.62
43_L	47_I	0.712	0.60
14_G	20_K	0.700	0.59
17_A	24_A	0.695	0.59
10_A	22_L	0.689	0.58
19_M	43_L	0.686	0.58
11_I	36_V	0.685	0.57
23_A	31_A	0.684	0.57
32_E	36_V	0.654	0.54
34_G	41_E	0.631	0.51
4_G	10_A	0.625	0.51
8_Q	12_A	0.623	0.51
37_R	51_E	0.620	0.50
22_L	29_H	0.608	0.49
20_K	41_E	0.605	0.48
41_E	44_K	0.592	0.47
24_A	37_R	0.591	0.47
33_H	38_A	0.589	0.47
16_L	30_L	0.583	0.46
37_R	41_E	0.578	0.45
32_E	42_A	0.575	0.45
23_A	44_K	0.568	0.44
26_A	47_I	0.561	0.44
39_A	42_A	0.556	0.43
17_A	21_A	0.543	0.42
14_G	19_M	0.536	0.41
29_H	40_L	0.531	0.40
1_P	5_V	0.531	0.40
19_M	26_A	0.525	0.40
25_Q	43_L	0.525	0.40
5_V	8_Q	0.515	0.39
5_V	9_E	0.506	0.38
35_D	48_A	0.500	0.37

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
2ra1A	1	0.9615	44.6	0.807	Contact Map
2a26A	4	0.9038	33.4	0.821	Contact Map
2hg7A	1	0.0769	27.6	0.828	Contact Map
3bbpD	2	0.6923	23.7	0.833	Contact Map
3t5vB	1	0.9808	20.5	0.838	Contact Map
1kd8A	1	0.6731	18.9	0.841	Contact Map
4cr2S	1	0.9231	18.7	0.841	Contact Map
1ysmA	1	0.8654	17.6	0.843	Contact Map
2iu8A	3	0.8654	15.1	0.847	Contact Map
3x2dB	3	0.9423	14.7	0.849	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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