Rv3465 dTDP-4-dehydrorhamnose 3,5-epimerase (EC 5.1.3.13)

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3465 rmlC dTDP-4-dehydrorhamnose 3,5-epimerase (EC 5.1.3.13) CDS 3882834 3883442 + 609 202 FALSE

Rv3465 (dTDP-4-dehydrorhamnose 3,5-epimerase (EC 5.1.3.13)) is predicted to be co-regulated in modules bicluster_0255 with residual 0.52 and bicluster_0491 with residual 0.60.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 3.80 for bicluster_0255 and 0.01 and 4,200.00 for bicluster_0491 respectively.

These modules are enriched for following go terms: .

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
No results were found
Motif 1 Motif 2 Residual
bicluster_0255
e.value: 
0.000011
Motif Bicluster: 
e.value: 
3.8
Motif Bicluster: 
0.52
bicluster_0491
e.value: 
0.0056
Motif Bicluster: 
e.value: 
4200
Motif Bicluster: 
0.60
Product (LegacyBRC) Product (RefSeq)
dTDP-4-DEHYDRORHAMNOSE 35-EPIMERASE RMLC [DTDP-4-KETO-6-DEOXYGLUCOSE 35-EPIMERASE] [DTDP-L-RHAMNOSE SYNTHETASE] [THYMIDINE DIPHOSPHO-4-KETO-RHAMNOSE 35-EPIMERASE] dTDP-4-dehydrorhamnose 3,5-epimerase RmlC
Operon # Operon
2264 -
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Streptomycin biosynthesis

12
Total items in this category:  

KEGG

Polyketide sugar unit biosynthesis

6
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
15610601 NP_217982.1 Run
GO:0008830

dTDP-4-dehydrorhamnose 3,5-epimerase activity

dTDP-4-dehydrorhamnose 3,5-epimerase activity

Details: 
Catalysis of the reaction: dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-L-mannose.
GO Category: 
molecular_function
1
Total items in this category:  
GO:0008830

dTDP-4-dehydrorhamnose 3,5-epimerase activity

dTDP-4-dehydrorhamnose 3,5-epimerase activity

Details: 
Catalysis of the reaction: dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-L-mannose.
GO Category: 
molecular_function
1
Total items in this category:  
GO:0019305

dTDP-rhamnose biosynthetic process

dTDP-rhamnose biosynthetic process

Details: 
The chemical reactions and pathways resulting in the formation of dTDP-rhamnose, a substance composed of rhamnose in glycosidic linkage with deoxyribosylthymine diphosphate.
GO Category: 
biological_process
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:  
GO:0042803

protein homodimerization activity

protein homodimerization activity

Details: 
Interacting selectively and non-covalently with an identical protein to form a homodimer.
GO Category: 
molecular_function
83
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: