Rv2539c Shikimate kinase I (EC 2.7.1.71)

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv2539c aroK Shikimate kinase I (EC 2.7.1.71) CDS 2862673 2863203 - 531 176 FALSE

Rv2539c (Shikimate kinase I (EC 2.7.1.71)) is predicted to be co-regulated in modules bicluster_0252 with residual 0.55 and bicluster_0399 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 930.00 and 3,100.00 for bicluster_0252 and 570.00 and 670.00 for bicluster_0399 respectively.

These modules are enriched for following go terms: regulation of cell shape, regulation of anatomical structure morph..., regulation of cell morphogenesis, regulation of developmental process, cell morphogenesis, anatomical structure morphogenesis, developmental process, cellular component morphogenesis, single-organism developmental process, anatomical structure development, cellular developmental process, regulation of cellular component organiz..., cellular component organization branched-chain amino acid metabolic proc....

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, AsnC family
No 23 -0.07 0.948053 CDS
Motif 1 Motif 2 Residual
bicluster_0252
e.value: 
930
Motif Bicluster: 
e.value: 
3100
Motif Bicluster: 
0.55
bicluster_0399
e.value: 
570
Motif Bicluster: 
e.value: 
670
Motif Bicluster: 
0.58
Product (LegacyBRC) Product (RefSeq)
Shikimate kinase shikimate kinase
Operon # Operon
1670 - - -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Shikimate kinase Phenylalanine, tyrosine and tryptophan biosynthesis
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Phenylalanine, tyrosine and tryptophan biosynthesis

18
Total items in this category:  

KEGG

Metabolic pathways

601
Total items in this category:  

KEGG

Biosynthesis of secondary metabolites

326
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15609676 NP_217055.1 Run
GO:0004765

shikimate kinase activity

shikimate kinase activity

Details: 
Catalysis of the reaction: ATP + shikimate = 3-phosphoshikimate + ADP + 2 H(+).
GO Category: 
molecular_function
1
Total items in this category:  
GO:0004765

shikimate kinase activity

shikimate kinase activity

Details: 
Catalysis of the reaction: ATP + shikimate = 3-phosphoshikimate + ADP + 2 H(+).
GO Category: 
molecular_function
1
Total items in this category:  
GO:0040007

growth

growth

Details: 
The increase in size or mass of an entire organism, a part of an organism or a cell.
GO Category: 
biological_process
621
Total items in this category:  
Description:Expression data from transcription factor over expression experiments. TFOE are matched to the ChIP-seq experiment done simultaneously. This dataset is described in Rustad et al. 2014, Genome Biology.
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
NA NA

How essentiality calculations were done?

The relative representation of each mutant was determined by calculating the fold change (sequence reads/insertion in cholesterol divided by sequence reads/insertion in glycerol) for each gene. Statistical significance was determined by t-test. Each insertion site in each replicate sample was treated as a separate data point. The hyperbola used for defining genes specifically required for growth in cholesterol was defined by the formula, y = 3.8/x+0.7. Genes above this line are annotated as required for growth on cholesterol.

TRIP log2 fold abundance change

reports the log2 abundance fold change of each TFI strain, relative to no induction, in absence or presence of drug, averaged across experimental replicates. Also reported are the accompanying z-scores and two-sided t-test p-values for each TFI strain under each condition. Please refer to Ma et al., 2020, Nature Microbiology for more information.

p-value Untreated:
p-value INH: