DUF4964 - PFAM28P - GREMLIN Contacts

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DUF4964 - Domain of unknown function (DUF4964)

PFAM:	PF16334	Sequences: LLLASCAAAQAADLFAPAAAQALRPPAVPLVTHDPYFSIWSPADKLTDSPTRHWTGKPHPLTGLIRVDGKTYRFMGKEPAPLKPILP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	87 (70)
Sequences:	1562 (1061)
Seq/√Len:	126.8
META:	0.929

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
63_G	74_F	4.008	1.00
45_K	48_D	3.808	1.00
49_S	52_R	3.407	1.00
43_A	49_S	3.279	1.00
64_L	71_T	3.186	1.00
27_A	42_P	3.150	1.00
33_H	37_F	3.094	1.00
39_I	51_T	2.384	1.00
42_P	52_R	2.246	1.00
24_R	28_V	2.180	1.00
46_L	75_M	2.015	1.00
50_P	60_P	1.704	1.00
42_P	56_G	1.548	1.00
73_R	78_E	1.536	1.00
39_I	59_H	1.492	1.00
39_I	61_L	1.332	1.00
66_R	71_T	1.294	1.00
34_D	53_H	1.213	0.99
38_S	41_S	1.209	0.99
43_A	52_R	1.181	0.99
32_T	53_H	1.178	0.99
16_A	20_A	1.177	0.99
42_P	49_S	1.134	0.99
52_R	58_P	1.116	0.99
50_P	62_T	1.076	0.99
50_P	58_P	1.068	0.99
24_R	44_D	1.045	0.98
19_A	22_A	1.031	0.98
36_Y	56_G	0.986	0.98
18_A	21_Q	0.954	0.97
65_I	74_F	0.942	0.97
15_F	18_A	0.940	0.97
37_F	56_G	0.926	0.96
25_P	28_V	0.920	0.96
38_S	55_T	0.905	0.96
38_S	54_W	0.901	0.96
63_G	75_M	0.890	0.96
64_L	74_F	0.887	0.95
37_F	51_T	0.886	0.95
15_F	19_A	0.878	0.95
47_T	64_L	0.866	0.95
77_K	80_A	0.864	0.95
33_H	56_G	0.836	0.94
31_V	53_H	0.814	0.93
51_T	60_P	0.791	0.92
66_R	81_P	0.783	0.91
30_L	61_L	0.780	0.91
35_P	38_S	0.779	0.91
27_A	50_P	0.767	0.91
23_L	57_K	0.766	0.91
80_A	83_K	0.764	0.90
50_P	77_K	0.760	0.90
81_P	84_P	0.753	0.90
41_S	51_T	0.735	0.89
47_T	84_P	0.707	0.87
58_P	79_P	0.683	0.85
34_D	41_S	0.662	0.83
29_P	40_W	0.658	0.83
15_F	20_A	0.647	0.82
32_T	57_K	0.647	0.82
67_V	84_P	0.642	0.81
23_L	28_V	0.635	0.80
16_A	19_A	0.624	0.79
25_P	41_S	0.624	0.79
50_P	65_I	0.622	0.79
27_A	52_R	0.600	0.77
64_L	80_A	0.600	0.77
40_W	53_H	0.585	0.75
31_V	37_F	0.585	0.75
50_P	78_E	0.577	0.74
47_T	51_T	0.574	0.73
25_P	30_L	0.572	0.73
42_P	60_P	0.569	0.73
24_R	46_L	0.564	0.72
62_T	73_R	0.564	0.72
26_P	74_F	0.559	0.71
49_S	77_K	0.554	0.71
41_S	53_H	0.553	0.71
32_T	59_H	0.551	0.70
70_K	83_K	0.551	0.70
30_L	37_F	0.549	0.70
31_V	55_T	0.547	0.70
18_A	58_P	0.545	0.69
33_H	53_H	0.545	0.69
43_A	48_D	0.544	0.69
22_A	27_A	0.541	0.69
67_V	72_Y	0.538	0.68
66_R	82_L	0.535	0.68
25_P	43_A	0.528	0.67
57_K	77_K	0.528	0.67
36_Y	75_M	0.525	0.67
19_A	81_P	0.525	0.67
71_T	79_P	0.524	0.66
39_I	47_T	0.520	0.66
65_I	82_L	0.518	0.66
53_H	61_L	0.518	0.66
39_I	55_T	0.518	0.66
28_V	43_A	0.516	0.65
65_I	83_K	0.515	0.65
33_H	51_T	0.514	0.65
69_G	77_K	0.513	0.65
33_H	60_P	0.513	0.65
31_V	61_L	0.504	0.63
18_A	70_K	0.504	0.63
37_F	62_T	0.500	0.63

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
4u6dA	2	0.7586	10.5	0.922	Contact Map
4g6tB	1	0.3333	8.4	0.925	Contact Map
3vsfA	1	0.931	8.2	0.926	Contact Map
3k7lA	1	0.4828	8.2	0.926	Contact Map
1yr2A	1	0.6552	7.5	0.927	Contact Map
2qarB	2	0.6552	5.7	0.931	Contact Map
2rsxA	1	0.7471	5.2	0.932	Contact Map
2ivfA	1	0.954	5.1	0.932	Contact Map
3g5cA	1	0.4023	4.8	0.934	Contact Map
3k7nA	1	0.4138	4.6	0.934	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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