DUF4911 - PFAM28P - GREMLIN Contacts

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DUF4911 - Domain of unknown function (DUF4911)

PFAM:	PF16256	Sequences: FRVDREDIAYLKFILEAYDGLAVVRTLDPKAGLVELLIAPDFEEEVRELLESLKKEI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	57 (55)
Sequences:	3606 (2537)
Seq/√Len:	342.1
META:	0.933

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_R	37_L	2.988	1.00
4_D	7_D	2.517	1.00
9_A	13_F	2.439	1.00
43_E	47_R	2.071	1.00
38_I	46_V	1.909	1.00
51_E	54_K	1.706	1.00
3_V	11_L	1.658	1.00
21_L	42_F	1.571	1.00
2_R	31_A	1.557	1.00
15_L	24_V	1.550	1.00
28_D	31_A	1.528	1.00
27_L	35_E	1.513	1.00
21_L	49_L	1.470	1.00
11_L	34_V	1.454	1.00
15_L	46_V	1.453	1.00
7_D	10_Y	1.430	1.00
49_L	53_L	1.388	1.00
12_K	16_E	1.369	1.00
36_L	46_V	1.334	1.00
38_I	43_E	1.326	1.00
10_Y	14_I	1.294	1.00
39_A	42_F	1.287	1.00
23_V	37_L	1.285	1.00
48_E	52_S	1.251	1.00
42_F	45_E	1.235	1.00
22_A	46_V	1.225	1.00
47_R	51_E	1.191	1.00
21_L	45_E	1.179	1.00
8_I	34_V	1.141	1.00
44_E	48_E	1.122	1.00
25_R	35_E	1.114	1.00
21_L	46_V	1.025	1.00
1_F	34_V	1.002	1.00
13_F	25_R	0.950	1.00
15_L	22_A	0.929	1.00
14_I	49_L	0.924	1.00
22_A	36_L	0.892	1.00
18_Y	49_L	0.862	1.00
38_I	42_F	0.839	1.00
48_E	51_E	0.827	1.00
16_E	27_L	0.808	1.00
27_L	33_L	0.808	1.00
45_E	48_E	0.806	1.00
8_I	32_G	0.771	1.00
10_Y	20_G	0.770	1.00
1_F	50_L	0.760	1.00
24_V	34_V	0.726	0.99
2_R	33_L	0.719	0.99
52_S	55_K	0.708	0.99
29_P	32_G	0.703	0.99
8_I	22_A	0.691	0.99
8_I	26_T	0.688	0.99
5_R	30_K	0.687	0.99
26_T	29_P	0.683	0.99
44_E	55_K	0.682	0.99
20_G	23_V	0.669	0.99
51_E	55_K	0.667	0.99
3_V	7_D	0.660	0.99
24_V	36_L	0.634	0.98
14_I	18_Y	0.631	0.98
14_I	17_A	0.630	0.98
12_K	23_V	0.595	0.98
9_A	12_K	0.577	0.97
28_D	32_G	0.573	0.97
1_F	38_I	0.565	0.97
17_A	32_G	0.564	0.97
8_I	24_V	0.561	0.97
16_E	25_R	0.552	0.96
3_V	27_L	0.550	0.96
23_V	35_E	0.550	0.96
14_I	53_L	0.543	0.96
3_V	9_A	0.537	0.96
10_Y	49_L	0.532	0.95
12_K	24_V	0.529	0.95
19_D	42_F	0.519	0.95
20_G	34_V	0.516	0.95
7_D	37_L	0.512	0.94
15_L	49_L	0.508	0.94
18_Y	53_L	0.505	0.94
6_E	9_A	0.504	0.94
35_E	51_E	0.502	0.94
11_L	53_L	0.500	0.94

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
2gjfA	2	1	31.4	0.796	Contact Map
1vjqA	2	1	23	0.809	Contact Map
1ayeA	1	1	20.2	0.814	Contact Map
1pcaA	1	1	17.3	0.819	Contact Map
2boaA	1	1	14.5	0.826	Contact Map
3f3fC	2	0.9298	11.6	0.833	Contact Map
3na7A	1	0.9123	11.5	0.833	Contact Map
3lapA	6	0.9474	11.3	0.834	Contact Map
3v4gA	5	0.8246	9.7	0.839	Contact Map
4p10A	1	0.9825	9.6	0.839	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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