DUF3848 - PFAM28P - GREMLIN Contacts

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DUF3848 - Protein of unknown function (DUF3848)

PFAM:	PF12959	Sequences: LNTKLYEKMEAEQEDFRDWLLSQPPEEILDHAYEITVKEDILMALEENDLSDEQAKALLKSPNPLADLYDEWLDRDTSHMDDLRDSIEDRADEVV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	95 (91)
Sequences:	912 (730)
Seq/√Len:	76.5
META:	0.934

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_E	38_K	3.219	1.00
25_P	28_I	2.915	1.00
21_L	26_E	2.481	1.00
9_M	42_L	2.436	1.00
13_Q	17_R	2.429	1.00
29_L	35_I	2.379	1.00
13_Q	38_K	2.162	1.00
61_S	67_D	2.098	1.00
19_W	23_Q	2.059	1.00
31_H	34_E	1.931	1.00
17_R	21_L	1.925	1.00
21_L	29_L	1.913	1.00
66_A	70_D	1.866	1.00
23_Q	31_H	1.843	1.00
17_R	29_L	1.805	1.00
20_L	29_L	1.715	1.00
54_Q	92_D	1.661	1.00
73_L	76_D	1.619	1.00
23_Q	27_E	1.534	0.99
9_M	45_L	1.531	0.99
26_E	30_D	1.514	0.99
32_A	36_T	1.499	0.99
40_D	80_M	1.499	0.99
2_N	55_A	1.439	0.99
72_W	75_R	1.384	0.99
63_N	66_A	1.374	0.99
38_K	66_A	1.358	0.98
11_A	15_D	1.348	0.98
10_E	14_E	1.343	0.98
33_Y	72_W	1.289	0.98
16_F	35_I	1.271	0.98
41_I	68_L	1.256	0.97
24_P	27_E	1.256	0.97
5_L	55_A	1.251	0.97
9_M	64_P	1.249	0.97
3_T	7_E	1.247	0.97
37_V	79_H	1.241	0.97
85_D	89_D	1.240	0.97
20_L	35_I	1.200	0.96
32_A	35_I	1.175	0.96
81_D	84_R	1.102	0.94
22_S	26_E	1.090	0.94
41_I	69_Y	1.051	0.93
61_S	64_P	1.051	0.93
75_R	89_D	1.046	0.93
50_L	54_Q	1.042	0.92
13_Q	35_I	1.038	0.92
41_I	83_L	1.014	0.91
84_R	88_E	0.965	0.89
72_W	86_S	0.964	0.89
72_W	78_S	0.934	0.88
89_D	92_D	0.927	0.87
43_M	46_E	0.922	0.87
20_L	31_H	0.922	0.87
16_F	36_T	0.914	0.86
71_E	90_R	0.910	0.86
57_A	61_S	0.903	0.86
11_A	18_D	0.898	0.86
16_F	20_L	0.878	0.84
52_D	56_K	0.860	0.83
38_K	69_Y	0.840	0.81
17_R	35_I	0.839	0.81
14_E	17_R	0.831	0.81
33_Y	69_Y	0.804	0.79
40_D	79_H	0.783	0.77
63_N	67_D	0.782	0.77
70_D	73_L	0.776	0.76
19_W	31_H	0.774	0.76
78_S	82_D	0.769	0.75
48_N	54_Q	0.764	0.75
75_R	86_S	0.764	0.75
2_N	6_Y	0.759	0.74
38_K	42_L	0.752	0.74
19_W	28_I	0.748	0.73
45_L	48_N	0.746	0.73
5_L	59_L	0.735	0.72
9_M	59_L	0.732	0.72
20_L	28_I	0.727	0.71
68_L	87_I	0.726	0.71
51_S	92_D	0.725	0.71
2_N	8_K	0.719	0.70
86_S	90_R	0.716	0.70
69_Y	73_L	0.711	0.70
15_D	19_W	0.705	0.69
16_F	19_W	0.694	0.68
71_E	74_D	0.687	0.67
7_E	11_A	0.682	0.66
83_L	86_S	0.679	0.66
12_E	69_Y	0.670	0.65
12_E	57_A	0.669	0.65
78_S	83_L	0.663	0.64
12_E	63_N	0.659	0.64
4_K	59_L	0.650	0.63
67_D	90_R	0.647	0.62
8_K	33_Y	0.638	0.61
85_D	88_E	0.631	0.60
68_L	90_R	0.628	0.60
84_R	87_I	0.624	0.60
6_Y	42_L	0.611	0.58
3_T	10_E	0.608	0.58
28_I	39_E	0.606	0.57
10_E	13_Q	0.605	0.57
4_K	7_E	0.604	0.57
86_S	89_D	0.603	0.57
18_D	21_L	0.594	0.56
8_K	86_S	0.594	0.56
52_D	60_K	0.585	0.55
74_D	81_D	0.585	0.55
75_R	85_D	0.584	0.55
33_Y	76_D	0.582	0.54
5_L	64_P	0.578	0.54
66_A	69_Y	0.573	0.53
82_D	86_S	0.569	0.53
8_K	62_P	0.564	0.52
28_I	31_H	0.562	0.52
80_M	83_L	0.561	0.52
53_E	92_D	0.561	0.52
15_D	37_V	0.558	0.51
11_A	14_E	0.556	0.51
22_S	27_E	0.549	0.50
24_P	57_A	0.547	0.50
6_Y	10_E	0.544	0.49
74_D	77_T	0.542	0.49
12_E	61_S	0.540	0.49
16_F	55_A	0.539	0.49
84_R	91_A	0.531	0.48
22_S	30_D	0.530	0.48
15_D	27_E	0.527	0.47
33_Y	37_V	0.523	0.47
44_A	83_L	0.519	0.46
17_R	26_E	0.511	0.45
16_F	37_V	0.510	0.45
20_L	39_E	0.508	0.45
45_L	75_R	0.501	0.44
51_S	56_K	0.501	0.44
72_W	82_D	0.500	0.44

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
2o3lA	1	0.7895	19.6	0.872	Contact Map
2hh6A	2	0.8947	9.4	0.888	Contact Map
4jrbA	1	0.6632	6.4	0.897	Contact Map
3fxbA	1	0.9158	5.3	0.901	Contact Map
2o4tA	2	0.7368	5	0.902	Contact Map
4pfiA	1	0.9053	4.6	0.904	Contact Map
4n4uA	1	0.9474	4.5	0.904	Contact Map
4o94A	1	0.9368	4.2	0.905	Contact Map
3rh3A	1	0.9263	3.6	0.908	Contact Map
4pe3A	1	0.9579	3.6	0.908	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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