Rv3596c ATP-dependent Clp protease, ATP-binding subunit ClpC / Negative regulator of genetic competence clcC/mecB

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3596c clpC1 ATP-dependent Clp protease, ATP-binding subunit ClpC / Negative regulator of genetic competence... CDS 4038158 4040704 - 2 547 848 FALSE

Rv3596c (ATP-dependent Clp protease, ATP-binding subunit ClpC / Negative regulator of genetic competence clcC/mecB) is predicted to be co-regulated in modules bicluster_0158 with residual 0.52 and bicluster_0582 with residual 0.57.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 20,000.00 and 33,000.00 for bicluster_0158 and 0.07 and 0.22 for bicluster_0582 respectively.

These modules are enriched for following go terms: pyruvate dehydrogenase activity, pyruvate dehydrogenase (acetyl-transferr..., oxidoreductase activity, acting on the a... .

This gene is found to be for growth on cholesterol.

Mutant available?:

Product (LegacyBRC) Product (RefSeq)
Probable ATP-dependent Clp protease ATP-binding subunit ATP-dependent protease ATP-binding subunit ClpC1
Operon # Operon
2344
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

not assigned to any KEGG Pathway.
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
57117131 YP_177995.1 Run
GO:0006289

nucleotide-excision repair

nucleotide-excision repair

Details: 
A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
GO Category: 
biological_process
5
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:0004518

nuclease activity

nuclease activity

Details: 
Catalysis of the hydrolysis of ester linkages within nucleic acids.
GO Category: 
molecular_function
5
Total items in this category:  
GO:0019538

protein metabolic process

protein metabolic process

Details: 
The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
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:0005524

ATP binding

ATP binding

Details: 
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO Category: 
molecular_function
58
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: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:0016887

ATPase activity

ATPase activity

Details: 
Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
GO Category: 
molecular_function
25
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: