DUF4377 - PFAM28P - GREMLIN Contacts

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DUF4377 - Domain of unknown function (DUF4377)

PFAM:	PF14302	Sequences: EVAPETVDCVGVGPQKCLQVRESPDGEWQLFYDEIEGFTYEPGYEYVLRVKRTKVENPPADASSIRYVLVEVVSK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	75 (75)
Sequences:	2580 (2000)
Seq/√Len:	231.0
META:	0.836

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
52_R	65_I	3.058	1.00
9_C	17_C	2.450	1.00
51_K	68_V	2.361	1.00
49_R	71_E	2.319	1.00
6_T	18_L	2.244	1.00
8_D	16_K	2.219	1.00
53_T	68_V	2.154	1.00
44_Y	75_K	1.905	1.00
69_L	72_V	1.855	1.00
55_V	58_P	1.780	1.00
59_P	62_A	1.691	1.00
52_R	67_Y	1.691	1.00
31_F	67_Y	1.683	1.00
2_V	20_V	1.670	1.00
47_V	74_S	1.642	1.00
36_E	68_V	1.631	1.00
36_E	66_R	1.564	1.00
40_Y	46_Y	1.552	1.00
2_V	48_L	1.544	1.00
6_T	16_K	1.458	1.00
53_T	66_R	1.419	1.00
1_E	21_R	1.348	1.00
16_K	42_P	1.330	1.00
47_V	73_V	1.302	1.00
22_E	29_Q	1.275	1.00
55_V	66_R	1.263	1.00
21_R	28_W	1.259	1.00
4_P	45_E	1.205	1.00
41_E	75_K	1.198	1.00
5_E	42_P	1.190	1.00
3_A	45_E	1.174	1.00
51_K	70_V	1.171	1.00
7_V	19_Q	1.165	1.00
41_E	44_Y	1.118	1.00
38_F	46_Y	1.116	1.00
22_E	52_R	1.102	1.00
23_S	26_G	1.099	1.00
49_R	70_V	1.086	1.00
54_K	65_I	1.069	1.00
21_R	45_E	1.064	1.00
3_A	19_Q	1.041	1.00
1_E	45_E	1.016	1.00
37_G	69_L	0.982	1.00
19_Q	30_L	0.979	1.00
1_E	24_P	0.978	1.00
33_D	63_S	0.926	1.00
10_V	14_P	0.915	1.00
5_E	19_Q	0.896	0.99
12_V	61_D	0.869	0.99
58_P	62_A	0.858	0.99
12_V	15_Q	0.847	0.99
60_A	63_S	0.840	0.99
35_I	69_L	0.840	0.99
18_L	34_E	0.836	0.99
1_E	47_V	0.829	0.99
20_V	31_F	0.829	0.99
54_K	64_S	0.814	0.99
1_E	23_S	0.812	0.99
31_F	34_E	0.793	0.99
28_W	45_E	0.779	0.98
11_G	32_Y	0.776	0.98
48_L	69_L	0.766	0.98
46_Y	72_V	0.761	0.98
6_T	34_E	0.759	0.98
26_G	29_Q	0.744	0.98
72_V	75_K	0.727	0.98
3_A	21_R	0.715	0.97
38_F	69_L	0.712	0.97
21_R	27_E	0.707	0.97
21_R	26_G	0.704	0.97
11_G	14_P	0.696	0.97
10_V	61_D	0.694	0.97
15_Q	32_Y	0.691	0.97
8_D	14_P	0.685	0.97
32_Y	59_P	0.671	0.96
5_E	47_V	0.661	0.96
40_Y	45_E	0.660	0.96
33_D	67_Y	0.640	0.95
22_E	26_G	0.637	0.95
11_G	15_Q	0.636	0.95
54_K	58_P	0.635	0.95
1_E	25_D	0.629	0.95
10_V	13_G	0.628	0.95
19_Q	28_W	0.624	0.94
60_A	64_S	0.617	0.94
4_P	42_P	0.613	0.94
51_K	66_R	0.604	0.93
46_Y	69_L	0.598	0.93
55_V	64_S	0.596	0.93
3_A	6_T	0.585	0.92
58_P	61_D	0.572	0.91
55_V	59_P	0.569	0.91
27_E	57_N	0.568	0.91
21_R	47_V	0.564	0.91
13_G	16_K	0.554	0.90
46_Y	75_K	0.553	0.90
49_R	73_V	0.549	0.90
50_V	67_Y	0.549	0.90
55_V	62_A	0.544	0.89
71_E	74_S	0.543	0.89
2_V	46_Y	0.542	0.89
20_V	29_Q	0.529	0.88
34_E	66_R	0.527	0.88
71_E	75_K	0.526	0.88
38_F	41_E	0.512	0.86
70_V	74_S	0.510	0.86
7_V	30_L	0.507	0.86
39_T	71_E	0.505	0.85
58_P	64_S	0.502	0.85
61_D	64_S	0.502	0.85
1_E	22_E	0.501	0.85
57_N	64_S	0.500	0.85

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
3cjlA	2	0.4	6.4	0.887	Contact Map
1cx1A	1	0.9867	3.2	0.902	Contact Map
4hsaC	1	0.92	3.1	0.903	Contact Map
4kw3A	1	0.4667	2.5	0.908	Contact Map
2c4xA	1	0.52	2	0.913	Contact Map
4gl2A	1	0.4133	1.8	0.915	Contact Map
3e9vA	1	0.3333	1.7	0.916	Contact Map
2qqpA	9	0.8	1.7	0.916	Contact Map
4mgqA	1	0.9867	1.6	0.917	Contact Map
1pc6A	2	0.7733	1.6	0.917	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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