YlbE - PFAM28P - GREMLIN Contacts

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YlbE - YlbE-like protein

PFAM:	PF14003	Sequences: PELKRYLRENPYWYKYLNRNPESLKEFEEEMKEKYKLTTPDKIEKFSNNIQMASMMLSMLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	61 (60)
Sequences:	531 (423)
Seq/√Len:	54.6
META:	0.682

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_Y	23_S	2.747	1.00
36_K	41_D	2.585	1.00
3_L	27_F	2.536	1.00
23_S	26_E	2.297	1.00
8_R	14_Y	2.075	1.00
24_L	27_F	2.017	1.00
46_F	50_I	1.993	1.00
15_K	19_R	1.824	0.99
3_L	31_M	1.727	0.99
31_M	35_Y	1.671	0.99
2_E	5_R	1.638	0.99
6_Y	30_E	1.553	0.98
33_E	38_T	1.517	0.98
5_R	9_E	1.513	0.98
15_K	18_N	1.506	0.97
36_K	45_K	1.491	0.97
38_T	41_D	1.451	0.97
3_L	24_L	1.387	0.96
24_L	28_E	1.338	0.95
4_K	7_L	1.338	0.95
7_L	27_F	1.331	0.95
25_K	28_E	1.312	0.94
14_Y	30_E	1.237	0.92
30_E	34_K	1.201	0.91
28_E	31_M	1.151	0.89
29_E	39_T	1.118	0.88
50_I	55_M	1.104	0.87
26_E	29_E	1.064	0.85
12_Y	30_E	1.061	0.85
20_N	23_S	1.031	0.83
16_Y	43_I	0.969	0.79
37_L	41_D	0.958	0.79
6_Y	34_K	0.949	0.78
13_W	30_E	0.935	0.77
19_R	35_Y	0.931	0.77
24_L	57_L	0.925	0.76
9_E	34_K	0.912	0.75
36_K	39_T	0.908	0.75
35_Y	41_D	0.895	0.74
45_K	60_L	0.894	0.74
44_E	48_N	0.873	0.72
9_E	35_Y	0.848	0.70
11_P	56_M	0.847	0.69
10_N	53_A	0.814	0.66
45_K	49_N	0.803	0.65
51_Q	55_M	0.798	0.65
8_R	48_N	0.796	0.65
7_L	11_P	0.793	0.64
53_A	60_L	0.788	0.64
10_N	32_K	0.777	0.63
10_N	34_K	0.767	0.62
29_E	45_K	0.767	0.62
12_Y	44_E	0.747	0.60
30_E	33_E	0.742	0.59
43_I	51_Q	0.712	0.56
23_S	46_F	0.695	0.54
43_I	50_I	0.693	0.54
28_E	32_K	0.692	0.54
11_P	59_M	0.672	0.52
20_N	33_E	0.671	0.52
15_K	37_L	0.664	0.51
9_E	19_R	0.664	0.51
44_E	47_S	0.654	0.50
29_E	38_T	0.640	0.48
8_R	13_W	0.640	0.48
28_E	35_Y	0.638	0.48
16_Y	26_E	0.637	0.48
12_Y	56_M	0.634	0.48
2_E	37_L	0.630	0.47
51_Q	58_S	0.628	0.47
11_P	51_Q	0.621	0.46
26_E	50_I	0.612	0.45
13_W	37_L	0.600	0.44
15_K	59_M	0.598	0.44
10_N	30_E	0.595	0.44
39_T	46_F	0.588	0.43
10_N	18_N	0.586	0.43
4_K	54_S	0.579	0.42
51_Q	54_S	0.561	0.40
46_F	49_N	0.560	0.40
40_P	50_I	0.554	0.39
11_P	55_M	0.554	0.39
11_P	21_P	0.536	0.37
18_N	31_M	0.533	0.37
11_P	40_P	0.531	0.37
15_K	35_Y	0.525	0.36
6_Y	52_M	0.525	0.36
8_R	56_M	0.519	0.36
50_I	56_M	0.511	0.35
13_W	23_S	0.500	0.34

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
3g06A	1	1	22.5	0.853	Contact Map
3e98A	2	0.2295	11.6	0.871	Contact Map
3cvrA	2	0.6066	11.3	0.872	Contact Map
4q68A	1	0.8525	10.6	0.873	Contact Map
2p1gA	1	0.8525	10.5	0.873	Contact Map
4lgyA	1	0.918	8.2	0.88	Contact Map
3ckdA	1	1	7.9	0.88	Contact Map
3hsqA	3	1	7.1	0.883	Contact Map
3ii2A	1	0.6885	6.9	0.884	Contact Map
4pufA	1	0.918	6	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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