Rv3286c RNA polymerase sigma factor SigB

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3286c sigF RNA polymerase sigma factor SigB CDS 3668169 3668954 - 786 261 TRUE

Rv3286c (RNA polymerase sigma factor SigB) is predicted to be co-regulated in modules bicluster_0127 with residual 0.45 and bicluster_0401 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.02 for bicluster_0127 and 100.00 and 180.00 for bicluster_0401 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 12
Gene Target Differential Expression Distance Expression pvalue Type
POSSIBLE METHYLTRANSFERASE CLUSTERED WITH NadR
Induced 69 1.2 0.000000417 CDS
Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
No -45 -0.21 0.648564 CDS
HIT family protein
Induced 64 1.53 0.000000000255 CDS
Induced -9 3.19 2.57839e-43 Primary.TSS
No -9 -0.03 0.923065 Antisense.TSS
No -97 -0.03 0.923065 Antisense.TSS
No 13 0.13 0.696765 CDS
No 33 0.13 0.696765 Antisense.TSS
Pyridoxine 5'-phosphate oxidase
No 49 -0.16 0.631941 CDS
PE family protein
No 8 0.98 0.0871189 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
ALTERNATE RNA POLYMERASE SIGMA FACTOR SIGF RNA polymerase sigma factor SigF
Operon # Operon
2149 -
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
15610422 NP_217803.1 Run
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: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: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:0006351

transcription, DNA-dependent

transcription, DNA-dependent

Details: 
The cellular synthesis of RNA on a template of DNA.
GO Category: 
biological_process
4
Total items in this category:  
GO:0006629

lipid metabolic process

lipid metabolic process

Details: 
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
GO Category: 
biological_process
3
Total items in this category:  
GO:0006979

response to oxidative stress

response to oxidative stress

Details: 
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
GO Category: 
biological_process
13
Total items in this category:  
GO:0006995

cellular response to nitrogen starvation

cellular response to nitrogen starvation

Details: 
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nitrogen.
GO Category: 
biological_process
4
Total items in this category:  
GO:0009409

response to cold

response to cold

Details: 
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
GO Category: 
biological_process
3
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 GSM1426968 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426969 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426970 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426968 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426969 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426970 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3286c_B404 UCSC Browser Tracks
Rv3286c_B534 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.050000 0.63

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: 0.00000000414334
p-value INH: 0.186888
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.39 U
D3I 3 3 3.83 11.99 I
D3U 3 3 3.83 12.45 U
D5I 9 5 6.00 8.07 I
D5U 17 5 6.00 10.69 U
D7I 18 7 8.14 8.19 I
D7U 19 7 8.14 11.98 U
D14I 4 14 15.63 3.18 I
D14U 4 14 15.63 11.21 U
D17I 3 17 19.15 2.26 I
D17U 3 17 19.15 11.13 U
D21I 4 21 23.23 I
D21U 4 21 23.23 9.11 U
D24I 3 24 26.60 I
D24U 3 24 26.60 10.44 U
D28I 4 28 30.61 1.11 I
D28U 4 28 30.61 8.63 U