Rv2703 RNA polymerase sigma factor SigB

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv2703 sigA RNA polymerase sigma factor SigB CDS 3017835 3019421 + 1 587 528 TRUE

Rv2703 (RNA polymerase sigma factor SigB) is predicted to be co-regulated in modules bicluster_0142 with residual 0.59 and bicluster_0271 with residual 0.56.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 420.00 and 7,300.00 for bicluster_0142 and 0.01 and 0.03 for bicluster_0271 respectively.

These modules are enriched for following go terms: DNA topological change, glutamate metabolic process, dicarboxylic acid biosynthetic process, DNA conformation change, DNA topoisomerase activity carboxylic acid biosynthetic process, organic acid biosynthetic process.

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 - 3 of 3
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, PadR family
No 64 -0.07 0.962221 Primary.TSS
Transcriptional regulator, ArsR family
No 65 0.2 0.109828 Primary.TSS
Transcriptional regulator, TetR family
No -147 0.16 0.522748 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0142
e.value: 
420
Motif Bicluster: 
e.value: 
7300
Motif Bicluster: 
0.59
bicluster_0271
e.value: 
0.013
Motif Bicluster: 
e.value: 
0.027
Motif Bicluster: 
0.56
Product (LegacyBRC) Product (RefSeq)
RNA polymerase sigma factor rpoD RNA polymerase sigma factor
Operon # Operon
1774 -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

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
15609840 NP_217219.1 Run
GO:0003700

sequence-specific DNA binding transcription factor activity

sequence-specific DNA binding transcription factor activity

Details: 
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
GO Category: 
molecular_function
17
Total items in this category:  
GO:0006355

regulation of transcription, DNA-dependent

regulation of transcription, DNA-dependent

Details: 
Any process that modulates the frequency, rate or extent of cellular DNA-dependent transcription.
GO Category: 
biological_process
15
Total items in this category:  
GO:0016987

sigma factor activity

sigma factor activity

Details: 
A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes.
GO Category: 
molecular_function
6
Total items in this category:  
GO:0030528

transcription regulator activity

transcription regulator activity

Details: 
OBSOLETE. Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor.
GO Category: 
molecular_function
1
Total items in this category:  
GO:0003677

DNA binding

DNA binding

Details: 
Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid).
GO Category: 
molecular_function
37
Total items in this category:  
GO:0006352

DNA-dependent transcription, initiation

DNA-dependent transcription, initiation

Details: 
Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
GO Category: 
biological_process
4
Total items in this category:  
GO:0003677

DNA binding

DNA binding

Details: 
Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid).
GO Category: 
molecular_function
37
Total items in this category:  
GO:0005515

protein binding

protein binding

Details: 
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
GO Category: 
molecular_function
135
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:0009405

pathogenesis

pathogenesis

Details: 
The set of specific processes that generate the ability of an organism to cause disease in another.
GO Category: 
biological_process
65
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.
BioProject Accession GEO Series References Repository Sample Method Sample Type
PRJNA254351 GSM1426850 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426851 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426852 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2703_B529 UCSC Browser Tracks
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: 0.558775
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D3I 3 3 3.83 13.68 I
D5I 9 5 6.00 12.73 I
D7I 18 7 8.14 13.09 I
D14I 4 14 15.63 12.27 I
D17I 3 17 19.15 11.23 I
D21I 4 21 23.23 10.78 I
D24I 3 24 26.60 9.70 I
D28I 4 28 30.61 9.36 I
D0U 27 0 0.00 13.52 U
D3U 3 3 3.83 14.24 U
D5U 17 5 6.00 12.97 U
D7U 19 7 8.14 13.06 U
D14U 4 14 15.63 13.21 U
D17U 3 17 19.15 12.98 U
D21U 4 21 23.23 13.03 U
D24U 3 24 26.60 12.90 U
D28U 4 28 30.61 12.78 U