DUF2282 - PFAM28P - GREMLIN Contacts

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DUF2282 - Predicted integral membrane protein (DUF2282)

PFAM:	PF10048	Sequences: KEKCYGVAKAGKNDCAAGAGTHSCAGTSKVDYDGNAWKYVPKGTCEKIVGGSL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	53 (51)
Sequences:	6964 (1691)
Seq/√Len:	236.8
META:	0.936

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_H	36_A	3.098	1.00
32_Y	49_V	2.691	1.00
2_E	43_G	2.308	1.00
22_H	27_T	2.123	1.00
30_V	33_D	1.961	1.00
15_C	24_C	1.581	1.00
17_A	21_T	1.533	1.00
1_K	41_P	1.529	1.00
9_K	31_D	1.518	1.00
40_V	44_T	1.464	1.00
33_D	36_A	1.396	1.00
18_G	21_T	1.392	1.00
23_S	27_T	1.366	1.00
9_K	32_Y	1.326	1.00
18_G	35_N	1.305	1.00
44_T	48_I	1.286	1.00
13_N	28_S	1.278	1.00
22_H	28_S	1.242	1.00
44_T	47_K	1.165	1.00
32_Y	50_G	1.154	1.00
27_T	36_A	1.144	1.00
28_S	36_A	1.116	1.00
19_A	35_N	1.105	1.00
41_P	44_T	1.085	1.00
2_E	40_V	1.081	1.00
21_T	35_N	1.050	1.00
16_A	37_W	1.043	1.00
9_K	12_K	1.043	1.00
38_K	48_I	1.027	1.00
28_S	33_D	1.020	1.00
16_A	25_A	1.000	1.00
46_E	49_V	0.986	1.00
1_K	5_Y	0.978	1.00
17_A	35_N	0.969	1.00
38_K	49_V	0.951	1.00
32_Y	38_K	0.949	1.00
7_V	48_I	0.932	1.00
5_Y	8_A	0.925	1.00
12_K	38_K	0.916	1.00
3_K	37_W	0.903	1.00
47_K	50_G	0.881	0.99
8_A	31_D	0.863	0.99
42_K	46_E	0.796	0.99
31_D	49_V	0.792	0.99
4_C	45_C	0.787	0.99
14_D	39_Y	0.774	0.99
38_K	50_G	0.763	0.98
14_D	38_K	0.762	0.98
25_A	37_W	0.736	0.98
17_A	22_H	0.736	0.98
40_V	43_G	0.720	0.98
7_V	40_V	0.720	0.98
41_P	47_K	0.708	0.97
20_G	37_W	0.689	0.97
11_G	44_T	0.653	0.96
11_G	31_D	0.627	0.95
8_A	40_V	0.615	0.94
38_K	44_T	0.604	0.94
17_A	20_G	0.595	0.93
3_K	27_T	0.583	0.93
16_A	27_T	0.579	0.92
38_K	41_P	0.573	0.92
10_A	29_K	0.570	0.92
18_G	34_G	0.568	0.92
12_K	46_E	0.560	0.91
2_E	42_K	0.555	0.91
17_A	25_A	0.549	0.90
5_Y	37_W	0.547	0.90
10_A	31_D	0.536	0.89
16_A	19_A	0.535	0.89
29_K	33_D	0.526	0.88
1_K	39_Y	0.524	0.88
17_A	36_A	0.513	0.87
6_G	26_G	0.513	0.87
5_Y	40_V	0.507	0.86
13_N	24_C	0.500	0.86

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
2ycuA	1	0.434	5	0.896	Contact Map
1wktA	1	0.8679	4.7	0.897	Contact Map
2kkxA	1	0.3396	1.2	0.925	Contact Map
1tujA	1	0.5849	1.2	0.925	Contact Map
3r1pA	1	0.7547	1.2	0.925	Contact Map
3vsfA	1	0.8868	1.2	0.926	Contact Map
2jp6A	1	0.2453	1.2	0.926	Contact Map
1oohA	1	0.6792	1.1	0.927	Contact Map
3jqoC	1	0.3962	1.1	0.927	Contact Map
4anjA	1	0.3585	1.1	0.928	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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