OPENSEQ.org - YFDK - ECOLI GREMLIN

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YFDK - Uncharacterized protein YfdK

UniProt:	P77656	Sequence MNYIYSATTNSFYPLEMKEDYTQAGSWPDDAVEVDEQVYIEFSGLPPKGKIRIAGENGFPAWSEIPPPTHEEQIAAAELKKQQLINQANDYMNSKQWAGKAAIGRLKGEELAQYNLWLDYLDALELVDTSSAPDIEWPTPPAVQAR	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG14135
Length:	146 (141)
Sequences:	327
Seq/Len:	2.32

YFDK
Paralog alert: 0.67 [within 20: 0.17] - ratio of genomes with paralogs
Cluster includes: TFAS YFDK YMFS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Scaled Score	Prob
80_K	84_L	2.873	1.00
99_G	121_L	2.528	1.00
6_S	30_D	2.07	0.99
100_K	106_L	1.972	0.99
108_G	111_L	1.96	0.99
118_L	122_D	1.822	0.98
122_D	126_L	1.813	0.98
88_A	117_W	1.771	0.98
118_L	121_L	1.752	0.98
78_E	129_T	1.749	0.98
106_L	122_D	1.738	0.98
5_Y	10_N	1.675	0.97
100_K	105_R	1.649	0.96
99_G	106_L	1.646	0.96
46_P	52_R	1.624	0.96
99_G	102_A	1.544	0.94
100_K	122_D	1.535	0.94
110_E	122_D	1.49	0.93
100_K	110_E	1.479	0.92
101_A	106_L	1.45	0.91
102_A	118_L	1.394	0.89
100_K	126_L	1.373	0.88
89_N	121_L	1.369	0.88
115_N	119_D	1.333	0.86
106_L	110_E	1.333	0.86
132_A	135_I	1.318	0.85
118_L	126_L	1.294	0.84
122_D	125_E	1.293	0.84
110_E	126_L	1.281	0.83
100_K	118_L	1.279	0.83
106_L	126_L	1.275	0.83
99_G	107_K	1.236	0.80
105_R	118_L	1.213	0.78
6_S	12_F	1.207	0.77
123_A	126_L	1.186	0.76
70_H	74_I	1.174	0.75
100_K	104_G	1.169	0.74
99_G	118_L	1.156	0.73
81_K	92_M	1.147	0.72
46_P	53_I	1.13	0.71
102_A	106_L	1.124	0.70
95_K	106_L	1.12	0.70
95_K	99_G	1.116	0.69
99_G	103_I	1.097	0.67
124_L	136_E	1.094	0.67
106_L	118_L	1.087	0.66
42_F	62_W	1.083	0.66
74_I	78_E	1.078	0.65
52_R	62_W	1.077	0.65
10_N	34_V	1.074	0.65
99_G	104_G	1.073	0.65
124_L	127_V	1.068	0.64
36_E	46_P	1.06	0.63
6_S	13_Y	1.052	0.63
102_A	115_N	1.052	0.63
78_E	81_K	1.05	0.62
105_R	122_D	1.045	0.62
100_K	121_L	1.044	0.62
119_D	122_D	1.04	0.61
47_P	52_R	1.04	0.61
95_K	125_E	1.03	0.60
41_E	66_P	1.026	0.60
100_K	119_D	1.025	0.60
102_A	121_L	1.025	0.60
32_V	36_E	1.017	0.59
42_F	45_L	1.01	0.58
110_E	118_L	1.002	0.57
101_A	121_L	1.002	0.57

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 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	P(%)	HHΔ		Acc
2kz6A	1	0.637	99.7	0.583	Contact Map	0.205
3kxyA	12	0.5274	3.1	0.954	Contact Map	0.57
3al0C	1	0.4178	2.6	0.956	Contact Map	0.438
1kjwA	1	0.8767	2.5	0.956	Contact Map	0.099
2q22A	3	0.6301	2.2	0.957	Contact Map	0.118
1jyoA	4	0.5411	2.2	0.958	Contact Map	0.514
3lsoA	1	0.3493	1.8	0.96	Contact Map	0.087
1dhkB	1	0.3219	1.5	0.961	Contact Map	0
2w84A	1	0.4658	1.4	0.962	Contact Map	0.435
1v54D	2	0.5205	1.4	0.962	Contact Map	0.19

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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