DUF1720 - PFAM28P - GREMLIN Contacts

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DUF1720 - Domain of unknown function (DUF1720)

PFAM:	PF08226	Sequences: LQPQPTGFQQPQQQQPQQQQPLQPQPTGFQPQQTGGQGLQPQPTGPGQFQPGLQPQPTGFQQQQQQPLQPQPTGF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	75 (74)
Sequences:	537 (466)
Seq/√Len:	54.1
META:	0.419

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_P	43_P	2.951	1.00
40_Q	54_Q	2.231	1.00
43_P	57_P	2.081	1.00
42_Q	56_Q	2.043	1.00
46_P	50_Q	2.022	1.00
25_Q	42_Q	1.987	1.00
60_F	75_F	1.962	1.00
43_P	72_P	1.958	1.00
39_L	53_L	1.952	1.00
41_P	55_P	1.921	1.00
56_Q	71_Q	1.894	0.99
57_P	72_P	1.808	0.99
53_L	68_L	1.762	0.99
42_Q	71_Q	1.746	0.99
31_P	34_T	1.726	0.99
54_Q	69_Q	1.701	0.99
25_Q	56_Q	1.694	0.99
63_Q	66_Q	1.689	0.99
11_P	14_Q	1.663	0.99
8_F	29_F	1.554	0.98
32_Q	35_G	1.552	0.98
26_P	57_P	1.551	0.98
5_P	26_P	1.509	0.97
22_L	53_L	1.508	0.97
4_Q	42_Q	1.433	0.96
40_Q	69_Q	1.407	0.96
4_Q	25_Q	1.361	0.95
24_P	41_P	1.232	0.92
3_P	70_P	1.231	0.92
26_P	72_P	1.170	0.90
23_Q	54_Q	1.151	0.89
72_P	75_F	1.123	0.88
4_Q	71_Q	1.075	0.86
12_Q	17_Q	1.064	0.85
44_T	58_T	1.034	0.83
5_P	43_P	0.992	0.81
32_Q	37_Q	0.954	0.78
38_G	67_P	0.945	0.77
46_P	49_F	0.945	0.77
6_T	58_T	0.943	0.77
39_L	68_L	0.938	0.77
32_Q	42_Q	0.929	0.76
57_P	60_F	0.912	0.75
22_L	39_L	0.907	0.74
30_Q	46_P	0.898	0.74
49_F	53_L	0.892	0.73
53_L	56_Q	0.884	0.72
3_P	41_P	0.880	0.72
32_Q	36_G	0.874	0.72
65_Q	71_Q	0.873	0.71
16_P	19_Q	0.847	0.69
45_G	74_G	0.844	0.69
31_P	35_G	0.831	0.68
11_P	32_Q	0.804	0.65
68_L	73_T	0.795	0.64
64_Q	69_Q	0.792	0.64
62_Q	70_P	0.785	0.63
29_F	60_F	0.774	0.62
62_Q	66_Q	0.768	0.61
41_P	70_P	0.765	0.61
64_Q	71_Q	0.753	0.60
15_Q	19_Q	0.747	0.59
63_Q	67_P	0.744	0.59
25_Q	71_Q	0.741	0.59
65_Q	72_P	0.725	0.57
9_Q	30_Q	0.723	0.57
3_P	6_T	0.709	0.55
10_Q	51_P	0.708	0.55
55_P	58_T	0.701	0.55
29_F	34_T	0.693	0.54
27_T	44_T	0.688	0.53
4_Q	7_G	0.687	0.53
9_Q	12_Q	0.676	0.52
13_Q	29_F	0.671	0.51
10_Q	13_Q	0.665	0.51
45_G	59_G	0.665	0.51
12_Q	15_Q	0.664	0.51
31_P	47_G	0.662	0.50
28_G	59_G	0.660	0.50
61_Q	64_Q	0.659	0.50
11_P	19_Q	0.646	0.49
37_Q	51_P	0.646	0.49
55_P	70_P	0.637	0.48
47_G	51_P	0.634	0.47
12_Q	18_Q	0.631	0.47
5_P	57_P	0.626	0.47
7_G	28_G	0.626	0.47
14_Q	17_Q	0.612	0.45
23_Q	40_Q	0.591	0.43
10_Q	31_P	0.586	0.42
8_F	60_F	0.583	0.42
64_Q	67_P	0.579	0.42
20_Q	26_P	0.578	0.42
9_Q	15_Q	0.567	0.40
52_G	67_P	0.561	0.40
11_P	15_Q	0.549	0.39
28_G	45_G	0.549	0.39
11_P	16_P	0.545	0.38
16_P	20_Q	0.543	0.38
10_Q	14_Q	0.543	0.38
61_Q	69_Q	0.540	0.38
61_Q	65_Q	0.536	0.37
3_P	35_G	0.531	0.37
6_T	73_T	0.528	0.36
44_T	73_T	0.527	0.36
38_G	52_G	0.517	0.35
53_L	58_T	0.516	0.35
62_Q	67_P	0.510	0.35
4_Q	56_Q	0.503	0.34
49_F	56_Q	0.502	0.34
33_Q	36_G	0.500	0.34

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
2lq1A	1	0.3333	1.1	0.893	Contact Map
2jx3A	1	0.0533	0.5	0.915	Contact Map
3g9hA	1	0.0267	0.4	0.922	Contact Map
3lvgA	3	0.0267	0.3	0.928	Contact Map
1k0hA	1	0.3333	0.3	0.93	Contact Map
3zh5A	1	0.32	0.2	0.94	Contact Map
2c7nA	1	0.12	0.2	0.941	Contact Map
3afhA	1	0.1733	0.2	0.942	Contact Map
4g6zA	1	0.1867	0.2	0.944	Contact Map
2qiyA	2	0.28	0.2	0.945	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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