Rv3911 RNA polymerase sigma-70 factor, ECF subfamily

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3911 sigM RNA polymerase sigma-70 factor, ECF subfamily CDS 4400186 4400854 + 669 222 TRUE

Rv3911 (RNA polymerase sigma-70 factor, ECF subfamily) is predicted to be co-regulated in modules bicluster_0476 with residual 0.52 and bicluster_0505 with residual 0.54.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.02 and 110.00 for bicluster_0476 and 0.00 and 0.00 for bicluster_0505 respectively.

These modules are enriched for following go terms: .

This gene is found to be essential for growth on cholesterol.

Mutant available?: Yes

BASS Score Distance to Tuberculist Start Codon Internal TSS New Internal UTR New Primary UTR Primary TSS Re-Annotated Start Tuberculist Annotated Start
-0.012 252 4400438 -222 121 4400095 4400216 4400186
Last update: 10/16/2017 - 16:54
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-15119 MT4030 1006
Displaying 1 - 2 of 2
Gene Target Differential Expression Distance Expression pvalue Type
DNA-binding protein
Induced -33 3.46 4.82005e-41 CDS
Conserved hypothetical protein
Induced -6 2.55 3.49063e-42 CDS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, PadR family
No 19 -0.12 0.772489 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0476
e.value: 
0.018
Motif Bicluster: 
e.value: 
110
Motif Bicluster: 
0.52
bicluster_0505
e.value: 
0.000016
Motif Bicluster: 
e.value: 
0.00038
Motif Bicluster: 
0.54
Product (LegacyBRC) Product (RefSeq)
POSSIBLE ALTERNATIVE RNA POLYMERASE SIGMA FACTOR SIGM RNA polymerase sigma factor SigM
Operon # Operon
2551 Rv3908 - Rv3909 - Rv3910 - Rv3911 - Rv3912
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
15611047 NP_218428.1 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: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: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: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:0009410

response to xenobiotic stimulus

response to xenobiotic stimulus

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 xenobiotic compound stimulus. Xenobiotic compounds are compounds foreign to living organisms.
GO Category: 
biological_process
4
Total items in this category:  
GO:0009415

response to water stimulus

response to water stimulus

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 stimulus reflecting the presence, absence, or concentration of water.
GO Category: 
biological_process
4
Total items in this category:  
GO:0045893

positive regulation of transcription, DNA-dependent

positive regulation of transcription, DNA-dependent

Details: 
Any process that activates or increases the frequency, rate or extent of cellular DNA-dependent transcription.
GO Category: 
biological_process
14
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 GSM1427060 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427061 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427062 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3911_B645 UCSC Browser Tracks
Quantitative Proteomics Data
Cholesterol Essentiality t-test p-value Cholesterol/Glycerol Ratio
essential 0.000000 0.26

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.

Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 14.33 U
D3I 3 3 3.83 14.55 I
D3U 3 3 3.83 14.55 U
D5I 9 5 6.00 14.30 I
D5U 17 5 6.00 14.59 U
D7I 18 7 8.14 14.61 I
D7U 19 7 8.14 15.38 U
D14I 4 14 15.63 14.47 I
D14U 4 14 15.63 16.95 U
D17I 3 17 19.15 13.01 I
D17U 3 17 19.15 17.20 U
D21I 4 21 23.23 11.94 I
D21U 4 21 23.23 16.81 U
D24I 3 24 26.60 10.51 I
D24U 3 24 26.60 16.95 U
D28I 4 28 30.61 9.63 I
D28U 4 28 30.61 16.53 U