OPENSEQ.org - YGDI - ECOLI GREMLIN

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YGDI - Uncharacterized lipoprotein YgdI

UniProt:	P65292	Sequence MKKTAAIISACMLTFALSACSGSNYVMHTNDGRTIVSDGKPQTDNDTGMISYKDANGNKQQINRTDVKEMVELDQ	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG13081
Length:	75 (74)
Sequences:	194
Seq/Len:	2.62

YGDI
Paralog alert: 0.92 [within 20: 0.06] - ratio of genomes with paralogs
Cluster includes: YGDI YGDR

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
4_T	8_I	1.68	0.98
24_N	39_G	1.589	0.96
3_K	10_A	1.542	0.95
40_K	61_Q	1.449	0.93
24_N	51_S	1.397	0.91
5_A	8_I	1.361	0.90
29_T	61_Q	1.338	0.89
1_M	62_I	1.326	0.88
12_M	21_S	1.31	0.87
44_D	47_T	1.264	0.84
25_Y	40_K	1.264	0.84
38_D	60_Q	1.26	0.84
34_T	74_D	1.243	0.83
2_K	75_Q	1.235	0.83
45_N	64_R	1.225	0.82
29_T	47_T	1.215	0.81
43_T	64_R	1.211	0.81
46_D	63_N	1.191	0.79
6_A	9_S	1.183	0.79
6_A	14_T	1.173	0.78
25_Y	37_S	1.167	0.77
30_N	68_K	1.165	0.77
10_A	58_N	1.156	0.76
1_M	13_L	1.138	0.75
43_T	50_I	1.125	0.74
3_K	13_L	1.124	0.74
31_D	68_K	1.121	0.73
28_H	49_M	1.116	0.73
53_K	74_D	1.109	0.72
6_A	70_M	1.088	0.70
11_C	19_A	1.087	0.70
24_N	36_V	1.067	0.68
36_V	49_M	1.051	0.66
2_K	18_S	1.037	0.65
42_Q	62_I	1.035	0.64
5_A	13_L	1.031	0.64
7_I	46_D	1.029	0.64
41_P	48_G	1.026	0.63
46_D	72_E	1.02	0.63
13_L	27_M	1.018	0.63
55_A	71_V	1.012	0.62
6_A	16_A	1.006	0.61
24_N	63_N	1.004	0.61
37_S	42_Q	1.001	0.61

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
2jn0A	1	0.7333	99.9	0.255	Contact Map	0.168
2rb6A	2	0.7333	99.9	0.257	Contact Map	0.278
3bduA	7	0.7333	99.9	0.261	Contact Map	0.39
2k57A	1	0.7333	99.9	0.261	Contact Map	0.222
2ra2A	6	0.7467	99.9	0.266	Contact Map	0.411
2rd1A	3	0.7333	99.9	0.267	Contact Map	0.28
3tlkA	3	0.6933	93.7	0.808	Contact Map	0
3ombA	1	1	88.1	0.833	Contact Map	0.047
1xt8A	2	0.9467	85.5	0.84	Contact Map	0.018
2yp6A	4	0.92	80	0.849	Contact Map	0.107

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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