Rv2388c Hypothetical radical SAM family enzyme in heat shock gene cluster, similarity with CPO of BS HemN-type

Summary

Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv2388c hemN Hypothetical radical SAM family enzyme in heat shock gene cluster, similarity with CPO of BS HemN-... CDS 2682015 2683142 - 1 128 375 FALSE

Rv2388c (Hypothetical radical SAM family enzyme in heat shock gene cluster, similarity with CPO of BS HemN-type) is predicted to be co-regulated in modules bicluster_0017 with residual 0.60 and bicluster_0543 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.25 and 10.00 for bicluster_0017 and 0.00 and 0.00 for bicluster_0543 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score Distance to Tuberculist Start Codon Internal TSS Primary TSS Re-Annotated Start Tuberculist Annotated Start
-1.324 847 2682295 2683187 2683187 2683142
Product (LegacyBRC) Product (RefSeq)
Probable oxygen-independent coproporphyrinogen III oxidase coproporphyrinogen III oxidase
Operon # Operon
1576
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Porphyrin and chlorophyll metabolism

31
Total items in this category:  

KEGG

Metabolic pathways

601
Total items in this category:  

KEGG

Biosynthesis of secondary metabolites

326
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15609525 NP_216904.1 Run
GO:0051989

coproporphyrinogen dehydrogenase activity

coproporphyrinogen dehydrogenase activity

Details: 
Catalysis of the reaction: coproporphyrinogen III + 2 S-adenosyl-L-methionine = protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine.
GO Category: 
molecular_function
1
Total items in this category:  
No TFOE experiment results were found

Quantitative Proteomics Data

t-test p-value Cholesterol/Glycerol Ratio
0.120000 8.06

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: