Rv3397c Phytoene synthase (EC

Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3397c phyA Phytoene synthase (EC CDS 3814090 3814998 - 909 302 FALSE

Rv3397c (Phytoene synthase (EC is predicted to be co-regulated in modules bicluster_0304 with residual 0.58 and bicluster_0568 with residual 0.57.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.36 and 78.00 for bicluster_0304 and 68.00 and 380.00 for bicluster_0568 respectively.

These modules are enriched for following go terms: cellular ketone metabolic process primary metabolic process, cellular metabolic process.

This gene is found to be for growth on cholesterol.

Mutant available?:

Product (LegacyBRC) Product (RefSeq)
Probable phytoene synthase phytoene synthase
Operon # Operon
2223 - -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics


Phytoene synthase Carotenoid biosynthesis
Locus Tuberculist Genome View


Locus Tag KEGG Pathways


Metabolic pathways

Total items in this category:  


Biosynthesis of secondary metabolites

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


GI Number Protein ID Blast Conserved Domains
15610533 NP_217914.1 Run

geranylgeranyl-diphosphate geranylgeranyltransferase activity

geranylgeranyl-diphosphate geranylgeranyltransferase activity

Catalysis of the reaction: 2 geranylgeranyl diphosphate = diphosphate + prephytoene diphosphate.
GO Category: 
Total items in this category:  
No TFOE experiment results were found
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.960000 1.50

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: