DUF3613 - PFAM28P - GREMLIN Contacts

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DUF3613 - Protein of unknown function (DUF3613)

PFAM:	PF12266	Sequences: QAIAAGPASPQQSEVGDATRAWLALQRSGRAASPTPQPATGAEAELAYQRYLKSFKHPIPEFFDQDA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	67 (59)
Sequences:	505 (341)
Seq/√Len:	44.4
META:	0.545

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_K	56_K	5.143	1.00
25_L	31_A	2.532	1.00
53_K	58_P	2.477	1.00
46_L	56_K	2.198	1.00
43_E	47_A	2.173	1.00
24_A	27_R	1.933	0.99
57_H	61_E	1.907	0.99
46_L	52_L	1.821	0.99
33_S	37_Q	1.742	0.98
24_A	28_S	1.704	0.98
8_A	11_Q	1.662	0.97
23_L	27_R	1.639	0.97
39_A	47_A	1.633	0.97
29_G	32_A	1.506	0.95
44_A	48_Y	1.494	0.95
48_Y	51_Y	1.398	0.93
41_G	55_F	1.358	0.92
37_Q	44_A	1.336	0.91
37_Q	40_T	1.318	0.91
25_L	28_S	1.300	0.90
41_G	51_Y	1.260	0.89
43_E	49_Q	1.221	0.87
39_A	44_A	1.219	0.87
7_P	11_Q	1.210	0.86
18_A	22_W	1.198	0.86
22_W	47_A	1.145	0.83
49_Q	53_K	1.135	0.83
9_S	12_Q	1.088	0.80
54_S	57_H	1.044	0.77
41_G	48_Y	0.964	0.71
14_E	17_D	0.960	0.71
22_W	25_L	0.949	0.70
21_A	45_E	0.888	0.65
8_A	12_Q	0.883	0.64
39_A	55_F	0.873	0.63
7_P	12_Q	0.865	0.63
7_P	10_P	0.859	0.62
42_A	46_L	0.838	0.60
15_V	44_A	0.814	0.58
40_T	59_I	0.789	0.56
29_G	33_S	0.785	0.55
22_W	31_A	0.773	0.54
16_G	44_A	0.758	0.53
7_P	34_P	0.748	0.52
33_S	45_E	0.743	0.51
27_R	30_R	0.743	0.51
35_T	38_P	0.736	0.50
51_Y	55_F	0.728	0.50
29_G	47_A	0.710	0.48
29_G	57_H	0.710	0.48
15_V	38_P	0.709	0.48
9_S	13_S	0.702	0.47
38_P	51_Y	0.698	0.47
45_E	64_D	0.683	0.45
20_R	45_E	0.672	0.44
13_S	17_D	0.655	0.43
57_H	62_F	0.647	0.42
39_A	42_A	0.642	0.41
37_Q	43_E	0.642	0.41
15_V	52_L	0.641	0.41
35_T	47_A	0.623	0.40
23_L	30_R	0.615	0.39
49_Q	56_K	0.604	0.38
52_L	56_K	0.597	0.37
10_P	20_R	0.595	0.37
14_E	25_L	0.580	0.36
39_A	43_E	0.579	0.36
23_L	60_P	0.575	0.35
28_S	31_A	0.573	0.35
34_P	59_I	0.556	0.34
28_S	53_K	0.553	0.33
50_R	60_P	0.553	0.33
20_R	57_H	0.551	0.33
37_Q	62_F	0.547	0.33
45_E	63_F	0.544	0.33
38_P	54_S	0.544	0.33
17_D	58_P	0.539	0.32
17_D	29_G	0.535	0.32
34_P	42_A	0.531	0.32
17_D	40_T	0.523	0.31
16_G	19_T	0.522	0.31
14_E	53_K	0.521	0.31
38_P	42_A	0.517	0.30
16_G	51_Y	0.510	0.30
31_A	61_E	0.510	0.30
56_K	61_E	0.502	0.29
12_Q	17_D	0.502	0.29
54_S	60_P	0.500	0.29

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
1ufiA	3	0.4925	5.6	0.902	Contact Map
3k0zA	2	0.6567	3.6	0.911	Contact Map
2lnjA	1	0.4627	3.2	0.913	Contact Map
1n4qB	2	0.403	2.9	0.915	Contact Map
2xb3A	1	0.3284	2.7	0.917	Contact Map
4ql6A	2	0.7761	2.5	0.918	Contact Map
2hsjA	3	0.4179	2.5	0.918	Contact Map
2ii3A	4	0.4776	2.4	0.918	Contact Map
2ec4A	1	0.4776	2.2	0.92	Contact Map
4pofA	3	0.4478	2.2	0.92	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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