DUF1724 - PFAM28P - GREMLIN Contacts

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DUF1724 - Domain of unknown function (DUF1724)

PFAM:	PF08350	Sequences: FKLYVYDEDIKKLALTVTDKFLSLGLFNKDGKYDYKDLISFDPSALKWGKELFEYYKKRSEP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	62 (59)
Sequences:	2226 (1550)
Seq/√Len:	201.8
META:	0.855

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_L	49_G	3.491	1.00
40_S	45_A	3.269	1.00
23_S	37_D	3.108	1.00
54_E	58_K	2.183	1.00
8_E	59_R	2.086	1.00
4_Y	57_K	1.939	1.00
7_D	61_E	1.903	1.00
22_L	45_A	1.700	1.00
21_F	41_F	1.669	1.00
17_V	49_G	1.608	1.00
25_G	33_Y	1.562	1.00
55_Y	59_R	1.553	1.00
25_G	37_D	1.493	1.00
46_L	50_K	1.492	1.00
53_F	57_K	1.486	1.00
6_Y	10_I	1.395	1.00
47_K	51_E	1.379	1.00
21_F	39_I	1.248	1.00
9_D	12_K	1.246	1.00
48_W	52_L	1.230	1.00
33_Y	45_A	1.229	1.00
43_P	47_K	1.193	1.00
44_S	50_K	1.106	1.00
6_Y	60_S	1.060	1.00
28_N	32_K	1.048	1.00
14_A	18_T	0.981	1.00
33_Y	37_D	0.978	1.00
35_Y	51_E	0.973	1.00
45_A	49_G	0.971	1.00
20_K	29_K	0.970	0.99
14_A	25_G	0.968	0.99
29_K	59_R	0.956	0.99
36_K	44_S	0.938	0.99
17_V	46_L	0.936	0.99
16_T	23_S	0.924	0.99
25_G	28_N	0.917	0.99
20_K	46_L	0.908	0.99
14_A	27_F	0.905	0.99
50_K	54_E	0.890	0.99
14_A	33_Y	0.868	0.99
7_D	12_K	0.855	0.99
39_I	49_G	0.839	0.99
4_Y	13_L	0.820	0.98
14_A	23_S	0.811	0.98
57_K	60_S	0.809	0.98
2_K	6_Y	0.807	0.98
34_D	38_L	0.803	0.98
2_K	5_V	0.780	0.98
27_F	33_Y	0.767	0.97
48_W	55_Y	0.748	0.97
40_S	46_L	0.739	0.97
27_F	49_G	0.734	0.97
16_T	53_F	0.727	0.96
29_K	61_E	0.715	0.96
56_Y	59_R	0.691	0.95
54_E	57_K	0.682	0.95
34_D	39_I	0.666	0.94
39_I	58_K	0.666	0.94
16_T	49_G	0.663	0.94
16_T	25_G	0.658	0.94
6_Y	9_D	0.657	0.94
4_Y	53_F	0.656	0.94
15_L	20_K	0.642	0.93
47_K	50_K	0.629	0.92
4_Y	51_E	0.624	0.92
13_L	34_D	0.622	0.92
4_Y	60_S	0.619	0.92
36_K	40_S	0.618	0.92
4_Y	8_E	0.614	0.91
7_D	54_E	0.613	0.91
15_L	33_Y	0.602	0.91
16_T	37_D	0.601	0.90
20_K	41_F	0.600	0.90
32_K	56_Y	0.591	0.90
14_A	49_G	0.590	0.90
46_L	49_G	0.569	0.88
31_G	58_K	0.563	0.87
13_L	16_T	0.559	0.87
22_L	42_D	0.548	0.86
14_A	17_V	0.544	0.86
27_F	38_L	0.537	0.85
47_K	58_K	0.536	0.85
2_K	8_E	0.536	0.85
3_L	8_E	0.533	0.84
6_Y	12_K	0.528	0.84
43_P	58_K	0.524	0.83
44_S	58_K	0.510	0.82
19_D	46_L	0.500	0.81

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
3qphA	2	0.9032	71	0.768	Contact Map
1byrA	2	0.9677	27.6	0.823	Contact Map
4ggjA	2	0.9839	24.5	0.828	Contact Map
4gelA	2	0.9677	8.9	0.859	Contact Map
1di1A	1	0.9516	8.7	0.86	Contact Map
3hsiA	2	1	8	0.862	Contact Map
4kwdA	2	0.9677	8	0.862	Contact Map
1z7lA	1	0.4194	7.1	0.865	Contact Map
3qweA	2	0.6774	6.8	0.867	Contact Map
1v0wA	1	0.9839	4.8	0.875	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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