Rv0113 Phosphoheptose isomerase (EC 5.3.1.-)

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0113 gmhA Phosphoheptose isomerase (EC 5.3.1.-) CDS 137319 137909 + 591 196 FALSE

Rv0113 (Phosphoheptose isomerase (EC 5.3.1.-)) is predicted to be co-regulated in modules bicluster_0150 with residual 0.60 and bicluster_0486 with residual 0.55.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.46 and 72.00 for bicluster_0150 and 500.00 and 840.00 for bicluster_0486 respectively.

These modules are enriched for following go terms: DNA binding, nucleic acid binding.

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 - 10 of 12
ChipSeq TF Differential Expression Distance Expression pvalue Type
DNA-binding response regulator TrcR
No -69 0.64 0.1038 CDS
Transcriptional regulator, IclR family
No -27 0.06 0.955092 CDS
Mn-dependent transcriptional regulator MntR
No -57 -0.22 0.548784 CDS
DNA-binding response regulator
No -55 0.26 0.40791 CDS
No -2 0.37 0.263716 CDS
Transcriptional regulator, TetR family
No -25 -0.27 0.643054 CDS
Transcriptional regulator, TetR family
No -46 -0.36 0.574859 CDS
putative two-component system response regulator
Induced -38 1.14 0.0000912 CDS
DNA-binding response regulator mtrA
No -148 0.05 0.973722 CDS
Transcriptional regulator, TetR family
Repressed -81 -0.81 0.0199056 CDS
Motif 1 Motif 2 Residual
bicluster_0150
e.value: 
0.46
Motif Bicluster: 
e.value: 
72
Motif Bicluster: 
0.60
bicluster_0486
e.value: 
500
Motif Bicluster: 
e.value: 
840
Motif Bicluster: 
0.55
Product (LegacyBRC) Product (RefSeq)
Phosphoheptose isomerase phosphoheptose isomerase
Operon # Operon
76 - -
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Lipopolysaccharide biosynthesis

3
Total items in this category:  

KEGG

Metabolic pathways

601
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15607255 NP_214627.1 Run
GO:0005975

carbohydrate metabolic process

carbohydrate metabolic process

Details: 
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
GO Category: 
biological_process
4
Total items in this category:  
GO:0005529

NA

NA

Details: 
NA
GO Category: 
NA
2
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
0.210000 0.77

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: