Rv0667 DNA-directed RNA polymerase beta subunit (EC 2.7.7.6)

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0667 rpoB DNA-directed RNA polymerase beta subunit (EC 2.7.7.6) CDS 759807 763325 + 3 519 1 172 FALSE

Rv0667 (DNA-directed RNA polymerase beta subunit (EC 2.7.7.6)) is predicted to be co-regulated in modules bicluster_0327 with residual 0.42 and bicluster_0354 with residual 0.44.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 440.00 and 980.00 for bicluster_0327 and 580.00 and 4,500.00 for bicluster_0354 respectively.

These modules are enriched for following go terms: monocarboxylic acid binding, protein tyrosine kinase activity, sulfur compound binding, protein kinase activity, amide binding .

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score Distance to Tuberculist Start Codon Internal TSS New Primary UTR Primary TSS Re-Annotated Start Tuberculist Annotated Start
-0.458 902 760709 197 759592 759789 759807
Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 10 of 14
ChipSeq TF Differential Expression Distance Expression pvalue Type
\Transcriptional regulator, XRE family\\\""
No 23 -0.04 0.929016 Primary.TSS
Transcriptional regulator, IclR family
No 24 0.06 0.999869 Primary.TSS
Histone protein Lsr2
No -33 0.07 0.868346 Primary.TSS
WhiB-like transcription regulator
No 8 0.14 0.999923 Primary.TSS
Transcriptional regulator, TetR family
No 35 0.02 0.963342 Primary.TSS
Transcriptional regulator, PadR family
No -16 -0.37 0.756087 Primary.TSS
Transcriptional regulator, TetR family
No -1 -0.09 0.89199 Primary.TSS
Transcriptional regulator, MarR family
No 34 0.03 0.956743 Primary.TSS
HTH-type transcriptional regulator
No -2 0.22 0.385095 Primary.TSS
Transcriptional regulator, TetR family
No 2 0.02 0.975135 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0327
e.value: 
440
Motif Bicluster: 
e.value: 
980
Motif Bicluster: 
0.42
bicluster_0354
e.value: 
580
Motif Bicluster: 
e.value: 
4500
Motif Bicluster: 
0.44
Product (LegacyBRC) Product (RefSeq)
DNA-directed RNA polymerase subunit beta DNA-directed RNA polymerase subunit beta
Operon # Operon
448
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

DNA-directed RNA polymerase Purine metabolism, Pyrimidine metabolism
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Purine metabolism

65
Total items in this category:  

KEGG

Pyrimidine metabolism

41
Total items in this category:  

KEGG

Metabolic pathways

601
Total items in this category:  

KEGG

RNA polymerase

17
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15607807 NP_215181.1 Run
GO:0003899

DNA-directed RNA polymerase activity

DNA-directed RNA polymerase activity

Details: 
Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
GO Category: 
molecular_function
5
Total items in this category:  
GO:0005618

cell wall

cell wall

Details: 
The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan.
GO Category: 
cellular_component
320
Total items in this category:  
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:  
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: