DUF3310 - PFAM28P - GREMLIN Contacts

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DUF3310 - Protein of unknwon function (DUF3310)

PFAM:	PF11753	Sequences: VNHPSHYKKGGIEPIDVIEANLGGEEFLGFCLGNAIKYIWRAGKKGGPLEDLKKAIWYLD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	60 (56)
Sequences:	21088 (11397)
Seq/√Len:	1523.0
META:	0.979

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_V	40_W	2.528	1.00
56_I	60_D	2.511	1.00
30_F	33_G	2.396	1.00
14_P	40_W	2.337	1.00
49_L	53_K	2.012	1.00
19_E	31_C	1.730	1.00
30_F	34_N	1.555	1.00
15_I	57_W	1.514	1.00
42_A	52_L	1.502	1.00
9_K	44_K	1.491	1.00
18_I	33_G	1.473	1.00
42_A	48_P	1.435	1.00
55_A	59_L	1.414	1.00
32_L	42_A	1.407	1.00
34_N	37_K	1.400	1.00
35_A	59_L	1.377	1.00
2_N	57_W	1.374	1.00
12_I	20_A	1.327	1.00
39_I	55_A	1.264	1.00
12_I	17_V	1.244	1.00
26_E	29_G	1.205	1.00
15_I	31_C	1.190	1.00
34_N	58_Y	1.176	1.00
35_A	39_I	1.160	1.00
26_E	32_L	1.140	1.00
11_G	20_A	1.139	1.00
3_H	57_W	1.116	1.00
29_G	32_L	1.103	1.00
17_V	21_N	1.089	1.00
46_G	50_E	1.087	1.00
10_G	44_K	1.071	1.00
39_I	59_L	1.068	1.00
46_G	51_D	1.003	1.00
32_L	43_G	0.994	1.00
57_W	60_D	0.992	1.00
35_A	55_A	0.988	1.00
19_E	27_F	0.977	1.00
43_G	48_P	0.960	1.00
21_N	40_W	0.950	1.00
50_E	53_K	0.934	1.00
47_G	50_E	0.933	1.00
14_P	18_I	0.929	1.00
25_E	28_L	0.929	1.00
53_K	56_I	0.905	1.00
18_I	36_I	0.870	1.00
14_P	36_I	0.859	1.00
49_L	56_I	0.847	1.00
56_I	59_L	0.838	1.00
21_N	36_I	0.803	1.00
36_I	40_W	0.783	1.00
4_P	57_W	0.727	1.00
43_G	51_D	0.721	1.00
13_E	16_D	0.716	1.00
27_F	31_C	0.710	1.00
47_G	51_D	0.709	1.00
37_K	58_Y	0.705	1.00
3_H	13_E	0.701	1.00
35_A	56_I	0.687	1.00
10_G	40_W	0.659	1.00
34_N	38_Y	0.656	1.00
12_I	16_D	0.638	1.00
32_L	48_P	0.631	1.00
52_L	59_L	0.613	1.00
15_I	30_F	0.606	1.00
18_I	30_F	0.602	1.00
29_G	33_G	0.601	1.00
15_I	19_E	0.592	1.00
28_L	32_L	0.592	1.00
17_V	36_I	0.591	1.00
10_G	20_A	0.588	1.00
43_G	47_G	0.586	1.00
17_V	20_A	0.585	1.00
3_H	8_K	0.579	1.00
10_G	14_P	0.579	1.00
43_G	46_G	0.575	1.00
9_K	12_I	0.565	1.00
38_Y	58_Y	0.541	1.00
5_S	8_K	0.533	1.00
30_F	58_Y	0.528	1.00
26_E	43_G	0.522	1.00
30_F	37_K	0.519	1.00
8_K	11_G	0.517	1.00
8_K	44_K	0.503	1.00
31_C	58_Y	0.500	1.00

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
3j9oB	7	0.9333	6.9	0.867	Contact Map
4wz9A	2	0.9167	5.8	0.872	Contact Map
1z5hA	3	0.9167	5.8	0.872	Contact Map
2d73A	2	0.8833	5.7	0.872	Contact Map
3b34A	1	0.9167	4.7	0.877	Contact Map
4qhpA	1	0.9167	4.3	0.879	Contact Map
5aj3G	1	1	4.2	0.88	Contact Map
4kx7A	1	0.9167	4.1	0.881	Contact Map
2yd0A	1	0.9	4	0.882	Contact Map
2dvkA	2	0.2	3.7	0.884	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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