Rv0003 DNA recombination and repair protein RecF

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0003 recF DNA recombination and repair protein RecF CDS 3280 4437 + 1 158 385 FALSE

Rv0003 (DNA recombination and repair protein RecF) is predicted to be co-regulated in modules bicluster_0128 with residual 0.56 and bicluster_0367 with residual 0.59.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.00 for bicluster_0128 and 0.00 and 0.00 for bicluster_0367 respectively.

These modules are enriched for following go terms: protein folding, propionyl-CoA carboxylase activity.

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 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, ArsR family
Induced 27 0.79 0.0000000000000725 Primary.TSS
Transcriptional regulator, IclR family
No 47 0 0.999076 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0128
e.value: 
0
Motif Bicluster: 
e.value: 
3.6e-35
Motif Bicluster: 
0.56
bicluster_0367
e.value: 
0.0000000000019
Motif Bicluster: 
e.value: 
0.00026
Motif Bicluster: 
0.59
Product (LegacyBRC) Product (RefSeq)
DNA replication and repair protein recF recombination protein F
Operon # Operon
2 - -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Homologous recombination

22
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15607145 NP_214517.1 Run
GO:0005829

cytosol

cytosol

Details: 
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO Category: 
cellular_component
371
Total items in this category:  
GO:0005886

plasma membrane

plasma membrane

Details: 
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO Category: 
cellular_component
1284
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
0.860000 1.76

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: