DUF4244 - PFAM28P - GREMLIN Contacts

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DUF4244 - Protein of unknown function (DUF4244)

PFAM:	PF14029	Sequences: RRLRRRLRDDAGMTTAEYAVGTLAAAAFAGLLYKVLTSDAVRGLLTGLIRRALS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	54 (50)
Sequences:	3219 (1779)
Seq/√Len:	251.5
META:	0.797

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
13_M	21_G	3.799	1.00
14_T	21_G	3.448	1.00
34_K	37_T	2.015	1.00
42_R	46_T	1.869	1.00
40_A	46_T	1.776	1.00
16_A	26_A	1.727	1.00
43_G	47_G	1.653	1.00
33_Y	37_T	1.580	1.00
39_D	42_R	1.553	1.00
22_T	30_G	1.541	1.00
6_R	9_D	1.491	1.00
48_L	53_L	1.462	1.00
28_F	36_L	1.452	1.00
46_T	50_R	1.437	1.00
16_A	22_T	1.372	1.00
7_L	11_A	1.269	1.00
38_S	42_R	1.240	1.00
27_A	33_Y	1.206	1.00
16_A	20_V	1.202	1.00
5_R	9_D	1.191	1.00
40_A	50_R	1.191	1.00
41_V	49_I	1.124	1.00
43_G	46_T	1.119	1.00
47_G	51_R	1.110	1.00
14_T	22_T	1.064	1.00
30_G	34_K	1.034	1.00
13_M	25_A	1.012	1.00
24_A	36_L	1.007	1.00
27_A	36_L	0.961	1.00
4_R	8_R	0.929	1.00
24_A	32_L	0.926	1.00
4_R	7_L	0.921	1.00
5_R	8_R	0.908	1.00
24_A	33_Y	0.881	1.00
23_L	33_Y	0.870	1.00
24_A	28_F	0.846	0.99
20_V	26_A	0.842	0.99
40_A	44_L	0.804	0.99
40_A	43_G	0.801	0.99
44_L	47_G	0.799	0.99
31_L	44_L	0.779	0.99
29_A	34_K	0.777	0.99
26_A	30_G	0.754	0.99
28_F	41_V	0.740	0.98
7_L	43_G	0.717	0.98
25_A	32_L	0.717	0.98
31_L	34_K	0.715	0.98
34_K	38_S	0.703	0.98
13_M	16_A	0.697	0.98
39_D	43_G	0.696	0.98
16_A	19_A	0.666	0.97
25_A	29_A	0.656	0.97
30_G	33_Y	0.651	0.96
6_R	11_A	0.646	0.96
13_M	22_T	0.640	0.96
22_T	26_A	0.609	0.95
19_A	26_A	0.593	0.94
29_A	32_L	0.584	0.94
23_L	26_A	0.581	0.93
29_A	41_V	0.581	0.93
35_V	41_V	0.574	0.93
47_G	50_R	0.569	0.93
34_K	42_R	0.565	0.93
32_L	38_S	0.561	0.92
15_T	32_L	0.551	0.92
44_L	48_L	0.546	0.91
27_A	31_L	0.543	0.91
10_D	31_L	0.536	0.90
8_R	11_A	0.536	0.90
15_T	18_Y	0.531	0.90
7_L	47_G	0.527	0.90
19_A	27_A	0.509	0.88
20_V	33_Y	0.509	0.88
12_G	17_E	0.509	0.88
43_G	50_R	0.500	0.87

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
4ytpD	1	0.7778	3.9	0.868	Contact Map
1xc0A	1	0.5	3.4	0.872	Contact Map
1elkA	1	0.4074	3.2	0.874	Contact Map
3ni7A	2	0.9259	3.1	0.875	Contact Map
2yicA	2	0.9444	3	0.875	Contact Map
2xt6A	2	0.9444	2.7	0.878	Contact Map
4ysxD	1	0.8704	2.1	0.886	Contact Map
4kxvA	2	0.8889	2	0.887	Contact Map
4puiA	1	0.3333	2	0.887	Contact Map
2x3nA	1	0.6667	2	0.887	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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