DUF4428 - PFAM28P - GREMLIN Contacts

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DUF4428 - Domain of unknown function (DUF4428)

PFAM:	PF14471	Sequences: NCDICGEKIGLLGNRKLEDGNLCKDCAKKLSPFFSDRRRKKQSTVEEIKEH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	51 (48)
Sequences:	632 (412)
Seq/√Len:	59.4
META:	0.85

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_E	25_D	2.924	1.00
46_E	50_E	2.693	1.00
4_I	22_L	2.610	1.00
30_L	48_I	2.230	1.00
2_C	5_C	2.117	1.00
14_N	21_N	2.003	1.00
18_E	39_R	1.791	0.99
46_E	49_K	1.740	0.99
45_V	49_K	1.702	0.99
34_F	43_S	1.625	0.99
47_E	50_E	1.544	0.98
30_L	43_S	1.509	0.98
15_R	37_R	1.441	0.97
15_R	27_A	1.378	0.97
3_D	20_G	1.335	0.96
3_D	45_V	1.328	0.96
15_R	24_K	1.180	0.92
6_G	36_D	1.166	0.92
9_I	20_G	1.116	0.90
17_L	22_L	1.066	0.88
21_N	24_K	1.063	0.88
31_S	35_S	1.011	0.85
9_I	14_N	0.984	0.83
30_L	33_F	0.968	0.82
28_K	39_R	0.959	0.82
32_P	43_S	0.956	0.81
27_A	37_R	0.942	0.80
28_K	36_D	0.934	0.80
3_D	21_N	0.903	0.77
17_L	23_C	0.902	0.77
14_N	22_L	0.891	0.77
14_N	17_L	0.830	0.71
9_I	21_N	0.826	0.71
35_S	39_R	0.818	0.70
9_I	13_G	0.804	0.69
12_L	24_K	0.794	0.68
13_G	32_P	0.774	0.66
3_D	10_G	0.769	0.65
30_L	34_F	0.760	0.64
12_L	16_K	0.758	0.64
7_E	10_G	0.754	0.64
43_S	48_I	0.743	0.63
18_E	42_Q	0.740	0.62
5_C	26_C	0.732	0.62
35_S	49_K	0.727	0.61
3_D	48_I	0.719	0.60
17_L	43_S	0.683	0.56
4_I	49_K	0.683	0.56
18_E	50_E	0.681	0.56
7_E	29_K	0.668	0.55
1_N	12_L	0.663	0.54
44_T	47_E	0.660	0.54
9_I	12_L	0.647	0.52
5_C	23_C	0.645	0.52
36_D	47_E	0.641	0.52
11_L	27_A	0.633	0.51
14_N	20_G	0.612	0.48
11_L	24_K	0.587	0.46
2_C	26_C	0.579	0.45
10_G	35_S	0.578	0.45
43_S	46_E	0.574	0.44
13_G	48_I	0.572	0.44
9_I	24_K	0.567	0.43
38_R	42_Q	0.566	0.43
13_G	20_G	0.554	0.42
10_G	13_G	0.552	0.42
4_I	24_K	0.540	0.40
8_K	11_L	0.537	0.40
36_D	43_S	0.514	0.38
23_C	26_C	0.504	0.37
19_D	45_V	0.502	0.36
2_C	23_C	0.500	0.36

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
3o9xA	2	1	72.2	0.703	Contact Map
2gviA	3	0.549	72.1	0.703	Contact Map
1ovxA	2	0.6863	71.5	0.705	Contact Map
2ds5A	2	0.7451	71.2	0.705	Contact Map
3d00A	2	0.5294	67.6	0.713	Contact Map
3avrA	1	1	47.9	0.745	Contact Map
4uf0A	2	1	47.5	0.746	Contact Map
4dduA	1	0.902	44.5	0.751	Contact Map
1y02A	1	0.902	43.5	0.752	Contact Map
2fiyA	1	0.9804	36.8	0.762	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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