Rv3458c SSU ribosomal protein S4p (S9e)

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3458c rpsD SSU ribosomal protein S4p (S9e) CDS 3878659 3879264 - 606 201 FALSE

Rv3458c (SSU ribosomal protein S4p (S9e)) is predicted to be co-regulated in modules bicluster_0327 with residual 0.42 and bicluster_0445 with residual 0.34.

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 920.00 and 3,100.00 for bicluster_0445 respectively.

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

This gene is found to be for growth on cholesterol.

Mutant available?:

Product (LegacyBRC) Product (RefSeq)
30S ribosomal protein S4 30S ribosomal protein S4
Operon # Operon
2261 - -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Ribosome

60
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15610594 NP_217975.1 Run
GO:0005622

intracellular

intracellular

Details: 
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
GO Category: 
cellular_component
65
Total items in this category:  
GO:0003723

RNA binding

RNA binding

Details: 
Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
GO Category: 
molecular_function
16
Total items in this category:  
GO:0003735

structural constituent of ribosome

structural constituent of ribosome

Details: 
The action of a molecule that contributes to the structural integrity of the ribosome.
GO Category: 
molecular_function
53
Total items in this category:  
GO:0005840

ribosome

ribosome

Details: 
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
GO Category: 
cellular_component
53
Total items in this category:  
GO:0006412

translation

translation

Details: 
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome.
GO Category: 
biological_process
62
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:  
No TFOE experiment results were found
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: