DUF413 - PFAM28P - GREMLIN Contacts

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DUF413 - Protein of unknown function, DUF

PFAM:	PF04219	Sequences: RFYDDKNFPRGFSRSGDFTIKEAQLLERYGVAMNALESGEREPETEEEKHFVAVCRGEREPETPLEKAWLKYLKRIRRPKRFHTLSGSKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	90 (88)
Sequences:	503 (298)
Seq/√Len:	31.7
META:	0.527

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
33_M	65_L	4.165	1.00
32_A	41_R	3.506	1.00
22_E	71_K	3.378	1.00
50_H	59_R	2.987	1.00
4_D	12_F	2.452	0.99
32_A	48_E	2.283	0.99
61_P	66_E	2.197	0.99
35_A	41_R	2.144	0.98
54_V	66_E	1.972	0.97
13_S	23_A	1.919	0.97
33_M	51_F	1.889	0.96
46_E	49_K	1.701	0.94
7_N	76_I	1.698	0.94
37_E	73_L	1.656	0.93
35_A	40_E	1.650	0.93
53_A	58_E	1.603	0.92
34_N	38_S	1.526	0.89
54_V	70_L	1.510	0.89
29_Y	32_A	1.486	0.88
10_R	15_S	1.482	0.88
32_A	35_A	1.462	0.87
43_P	52_V	1.461	0.87
18_F	26_L	1.428	0.86
54_V	61_P	1.421	0.86
38_S	49_K	1.389	0.84
43_P	48_E	1.320	0.81
5_D	19_T	1.261	0.78
27_E	32_A	1.235	0.76
13_S	24_Q	1.232	0.76
73_L	77_R	1.231	0.76
4_D	7_N	1.227	0.76
49_K	53_A	1.209	0.75
4_D	72_Y	1.164	0.72
27_E	41_R	1.162	0.72
82_F	85_L	1.138	0.70
25_L	68_A	1.129	0.70
15_S	18_F	1.099	0.68
25_L	63_T	1.067	0.65
25_L	65_L	1.061	0.65
49_K	62_E	1.053	0.64
5_D	10_R	1.013	0.61
64_P	68_A	0.992	0.60
8_F	18_F	0.951	0.56
12_F	72_Y	0.944	0.56
53_A	67_K	0.934	0.55
81_R	87_G	0.925	0.54
79_P	83_H	0.907	0.53
67_K	88_S	0.900	0.52
17_D	75_R	0.894	0.52
4_D	9_P	0.893	0.52
43_P	62_E	0.880	0.50
21_K	24_Q	0.867	0.49
10_R	22_E	0.866	0.49
83_H	86_S	0.864	0.49
82_F	86_S	0.859	0.49
53_A	59_R	0.856	0.49
41_R	48_E	0.847	0.48
30_G	69_W	0.844	0.48
76_I	82_F	0.844	0.48
41_R	44_E	0.826	0.46
8_F	33_M	0.825	0.46
36_L	52_V	0.822	0.46
50_H	63_T	0.820	0.46
74_K	78_R	0.810	0.45
43_P	51_F	0.809	0.45
41_R	55_C	0.802	0.44
78_R	86_S	0.801	0.44
10_R	19_T	0.800	0.44
14_R	37_E	0.797	0.44
9_P	45_T	0.796	0.44
57_G	64_P	0.791	0.43
12_F	79_P	0.764	0.41
83_H	88_S	0.761	0.41
54_V	63_T	0.760	0.41
49_K	67_K	0.755	0.40
75_R	78_R	0.748	0.40
2_F	8_F	0.746	0.40
26_L	53_A	0.736	0.39
80_K	87_G	0.722	0.38
54_V	57_G	0.719	0.38
56_R	63_T	0.718	0.38
37_E	55_C	0.706	0.37
2_F	14_R	0.694	0.36
31_V	63_T	0.691	0.35
82_F	87_G	0.669	0.34
16_G	30_G	0.665	0.34
85_L	88_S	0.657	0.33
34_N	37_E	0.649	0.32
59_R	62_E	0.647	0.32
60_E	67_K	0.643	0.32
22_E	39_G	0.641	0.32
6_K	43_P	0.619	0.30
82_F	88_S	0.613	0.30
15_S	24_Q	0.613	0.30
47_E	63_T	0.608	0.30
8_F	12_F	0.606	0.29
50_H	54_V	0.604	0.29
35_A	80_K	0.604	0.29
52_V	55_C	0.601	0.29
3_Y	24_Q	0.601	0.29
21_K	56_R	0.601	0.29
20_I	23_A	0.584	0.28
7_N	12_F	0.582	0.28
46_E	70_L	0.579	0.28
48_E	51_F	0.577	0.27
1_R	31_V	0.576	0.27
71_K	75_R	0.574	0.27
81_R	86_S	0.572	0.27
9_P	57_G	0.568	0.27
11_G	16_G	0.566	0.27
11_G	69_W	0.566	0.27
84_T	87_G	0.563	0.27
63_T	66_E	0.563	0.27
46_E	50_H	0.560	0.26
8_F	17_D	0.559	0.26
35_A	42_E	0.558	0.26
2_F	71_K	0.554	0.26
19_T	81_R	0.553	0.26
63_T	69_W	0.550	0.26
55_C	73_L	0.549	0.26
39_G	47_E	0.548	0.26
61_P	70_L	0.545	0.25
61_P	74_K	0.542	0.25
9_P	61_P	0.536	0.25
39_G	48_E	0.535	0.25
44_E	60_E	0.534	0.25
29_Y	41_R	0.532	0.25
25_L	61_P	0.532	0.25
14_R	67_K	0.520	0.24
50_H	66_E	0.514	0.24
50_H	62_E	0.513	0.24
10_R	16_G	0.500	0.23

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
2qdjA	1	0.4	38.4	0.899	Contact Map
4eljA	1	0.4222	18	0.914	Contact Map
3mwpA	2	0.9333	15.6	0.917	Contact Map
4o6iA	2	0.9333	13.9	0.919	Contact Map
2efvA	2	0.5	13.4	0.919	Contact Map
3q7cA	1	0.9333	13.2	0.919	Contact Map
4k7eA	2	0.6	11.8	0.921	Contact Map
4gveA	1	0.9111	11.3	0.922	Contact Map
3e6pL	1	0.3222	6.8	0.929	Contact Map
2wviA	1	0.6778	6.4	0.93	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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