DUF3794 - PFAM28P - GREMLIN Contacts

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DUF3794 - Domain of unknown function (DUF3794)

PFAM:	PF12673	Sequences: DIEKILKVDGKVRITEVKVIEDKVIVEGELEVQILYGPVHSLEGEIPFSQFIEIPGAEEGMIVDVKAEVEDIDVELI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	77 (74)
Sequences:	6596 (5355)
Seq/√Len:	622.5
META:	0.848

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
23_K	51_F	3.188	1.00
28_G	48_F	2.687	1.00
29_E	45_E	2.495	1.00
8_V	74_V	2.133	1.00
33_Q	41_S	2.058	1.00
10_G	72_I	2.019	1.00
20_I	23_K	1.965	1.00
54_I	57_A	1.935	1.00
15_T	29_E	1.899	1.00
13_R	31_E	1.879	1.00
20_I	25_I	1.859	1.00
32_V	46_I	1.811	1.00
31_E	45_E	1.759	1.00
16_E	27_E	1.692	1.00
33_Q	43_E	1.631	1.00
34_I	44_G	1.595	1.00
58_E	61_M	1.573	1.00
22_D	56_G	1.515	1.00
29_E	47_P	1.416	1.00
12_V	67_A	1.415	1.00
25_I	49_S	1.404	1.00
22_D	55_P	1.396	1.00
24_V	63_V	1.356	1.00
10_G	30_L	1.321	1.00
5_I	34_I	1.262	1.00
17_V	65_V	1.251	1.00
27_E	49_S	1.245	1.00
25_I	51_F	1.226	1.00
21_E	58_E	1.214	1.00
24_V	57_A	1.206	1.00
32_V	44_G	1.184	1.00
23_K	53_E	1.170	1.00
17_V	63_V	1.157	1.00
26_V	50_Q	1.134	1.00
21_E	59_E	1.122	1.00
36_Y	40_H	1.122	1.00
31_E	43_E	1.102	1.00
19_V	57_A	1.081	1.00
34_I	42_L	1.078	1.00
57_A	61_M	1.036	1.00
28_G	47_P	1.032	1.00
20_I	51_F	1.008	1.00
19_V	63_V	0.967	1.00
10_G	69_V	0.959	1.00
6_L	39_V	0.929	1.00
18_K	25_I	0.921	1.00
50_Q	53_E	0.915	1.00
71_D	74_V	0.913	1.00
13_R	29_E	0.899	1.00
12_V	69_V	0.895	1.00
18_K	59_E	0.877	1.00
9_D	33_Q	0.864	1.00
12_V	48_F	0.846	1.00
11_K	31_E	0.844	1.00
8_V	34_I	0.834	1.00
64_D	67_A	0.827	1.00
17_V	26_V	0.776	1.00
19_V	24_V	0.769	1.00
63_V	67_A	0.754	1.00
24_V	54_I	0.753	1.00
41_S	44_G	0.747	1.00
22_D	54_I	0.743	1.00
26_V	65_V	0.733	1.00
14_I	67_A	0.731	1.00
57_A	63_V	0.728	1.00
35_L	41_S	0.728	1.00
18_K	27_E	0.701	1.00
49_S	53_E	0.697	1.00
3_E	37_G	0.695	1.00
3_E	7_K	0.688	1.00
38_P	41_S	0.681	1.00
67_A	70_E	0.666	1.00
7_K	51_F	0.661	1.00
17_V	24_V	0.653	1.00
14_I	29_E	0.646	1.00
44_G	47_P	0.645	1.00
22_D	53_E	0.641	1.00
40_H	44_G	0.632	1.00
42_L	74_V	0.622	1.00
14_I	17_V	0.613	1.00
13_R	45_E	0.613	1.00
3_E	38_P	0.605	1.00
19_V	61_M	0.602	1.00
59_E	62_I	0.601	1.00
34_I	54_I	0.588	1.00
8_V	12_V	0.587	1.00
6_L	32_V	0.581	1.00
26_V	52_I	0.580	1.00
32_V	35_L	0.571	1.00
38_P	43_E	0.567	1.00
56_G	59_E	0.564	1.00
47_P	50_Q	0.564	1.00
12_V	30_L	0.563	1.00
10_G	32_V	0.560	1.00
4_K	33_Q	0.557	1.00
4_K	15_T	0.553	1.00
36_Y	70_E	0.553	1.00
6_L	9_D	0.552	1.00
64_D	68_E	0.548	1.00
10_G	28_G	0.547	1.00
19_V	33_Q	0.546	0.99
69_V	72_I	0.546	0.99
22_D	57_A	0.537	0.99
6_L	35_L	0.527	0.99
24_V	52_I	0.520	0.99
3_E	51_F	0.519	0.99
42_L	73_D	0.511	0.99
20_I	59_E	0.508	0.99
34_I	39_V	0.503	0.99
26_V	67_A	0.501	0.99
9_D	64_D	0.500	0.99

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
3vv1A	2	0.5584	2.8	0.869	Contact Map
3m9dG	1	0.1299	2.5	0.873	Contact Map
4un4B	1	0.6623	2.5	0.873	Contact Map
3m91B	1	0.1299	2.4	0.874	Contact Map
4qq0A	1	0.987	2.4	0.874	Contact Map
1b77A	3	0.8571	2.2	0.877	Contact Map
4m0nA	1	0.3896	1.9	0.881	Contact Map
1usuB	1	0.8961	1.8	0.882	Contact Map
3nv1A	1	0.4675	1.8	0.883	Contact Map
4alzA	1	0.7403	1.7	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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