DUF2783 - PFAM28P - GREMLIN Contacts

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DUF2783 - Protein of unknown function (DUF2783)

PFAM:	PF10932	Sequences: LNTEPNLADPDDFYEALIDAHRGLSDEQSAALNARLVLLLANHIGDLAVLREALAAARE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	59 (58)
Sequences:	4256 (2070)
Seq/√Len:	271.8
META:	0.917

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_D	12_D	2.879	1.00
26_D	30_A	2.838	1.00
16_A	51_R	2.822	1.00
20_A	32_L	2.796	1.00
25_S	28_Q	2.167	1.00
2_N	6_N	2.079	1.00
20_A	54_L	1.904	1.00
21_H	29_S	1.881	1.00
13_F	50_L	1.881	1.00
13_F	41_A	1.768	1.00
15_E	19_D	1.703	1.00
47_L	51_R	1.678	1.00
43_H	49_V	1.603	1.00
24_L	32_L	1.580	1.00
31_A	35_R	1.504	1.00
19_D	22_R	1.472	1.00
52_E	56_A	1.449	1.00
21_H	33_N	1.363	1.00
30_A	33_N	1.362	1.00
16_A	47_L	1.331	1.00
43_H	53_A	1.318	1.00
40_L	53_A	1.301	1.00
33_N	37_V	1.300	1.00
39_L	56_A	1.244	1.00
29_S	33_N	1.212	1.00
8_A	46_D	1.201	1.00
40_L	44_I	1.155	1.00
24_L	58_R	1.125	1.00
1_L	53_A	1.100	1.00
13_F	17_L	1.053	1.00
8_A	47_L	1.023	1.00
44_I	49_V	1.017	1.00
7_L	13_F	1.015	1.00
28_Q	31_A	0.965	1.00
41_A	50_L	0.934	1.00
1_L	43_H	0.848	1.00
9_D	47_L	0.833	0.99
16_A	55_A	0.814	0.99
32_L	35_R	0.775	0.99
39_L	57_A	0.740	0.99
3_T	52_E	0.737	0.99
24_L	28_Q	0.726	0.99
32_L	58_R	0.717	0.98
12_D	47_L	0.716	0.98
39_L	53_A	0.706	0.98
15_E	22_R	0.697	0.98
3_T	56_A	0.691	0.98
21_H	32_L	0.688	0.98
36_L	53_A	0.672	0.98
48_A	52_E	0.663	0.97
2_N	5_P	0.656	0.97
49_V	52_E	0.647	0.97
23_G	58_R	0.646	0.97
49_V	53_A	0.638	0.97
31_A	34_A	0.635	0.97
37_V	54_L	0.628	0.97
17_L	31_A	0.628	0.97
21_H	24_L	0.622	0.96
7_L	47_L	0.608	0.96
20_A	24_L	0.606	0.96
5_P	10_P	0.606	0.96
50_L	54_L	0.605	0.96
20_A	57_A	0.595	0.95
16_A	19_D	0.594	0.95
12_D	51_R	0.589	0.95
7_L	10_P	0.583	0.95
13_F	54_L	0.579	0.95
13_F	47_L	0.572	0.94
10_P	18_I	0.567	0.94
48_A	55_A	0.563	0.94
48_A	51_R	0.550	0.93
34_A	37_V	0.548	0.93
43_H	52_E	0.537	0.92
9_D	48_A	0.526	0.91
6_N	50_L	0.525	0.91
7_L	19_D	0.523	0.91
39_L	58_R	0.520	0.91
11_D	29_S	0.516	0.91
21_H	37_V	0.513	0.90
10_P	41_A	0.510	0.90
53_A	56_A	0.508	0.90
30_A	37_V	0.505	0.90
35_R	58_R	0.504	0.89
7_L	41_A	0.503	0.89
29_S	37_V	0.502	0.89
8_A	35_R	0.500	0.89
33_N	36_L	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
1khdA	2	0.9322	7.1	0.878	Contact Map
2xs1A	1	0.5932	6.1	0.881	Contact Map
4xgcC	1	0.8814	6.1	0.882	Contact Map
1c7cA	1	1	5.9	0.883	Contact Map
3pvsA	4	1	5.8	0.883	Contact Map
2r80A	2	1	5.5	0.884	Contact Map
4fhnB	1	0.9492	5.3	0.885	Contact Map
3bomB	1	1	5	0.887	Contact Map
1lhsA	1	1	5	0.887	Contact Map
2w72C	2	1	4.7	0.888	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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