Rv3060c Transcriptional regulator, GntR family

Product Feature Type Start End Strand Length AA Length is TF
Rv3060c Transcriptional regulator, GntR family CDS 3421741 3423213 - 1 473 490 TRUE

Rv3060c (Transcriptional regulator, GntR family) is predicted to be co-regulated in modules bicluster_0130 with residual 0.52 and bicluster_0580 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 130.00 and 570.00 for bicluster_0130 and 0.00 and 0.19 for bicluster_0580 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Product (LegacyBRC) Product (RefSeq)
Operon # Operon
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics


Not assigned Not assigned
Locus Tuberculist Genome View


Locus Tag KEGG Pathways


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


GI Number Protein ID Blast Conserved Domains
15610197 NP_217576.1 Run

cell wall

cell wall

The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan.
GO Category: 
Total items in this category:  

plasma membrane

plasma membrane

The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO Category: 
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 GSM1426904 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426905 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426906 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3060c_B123 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.210000 1.16

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:
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 5.66 U
D3I 3 3 3.83 11.00 I
D3U 3 3 3.83 11.55 U
D5I 9 5 6.00 I
D5U 17 5 6.00 U
D7I 18 7 8.14 4.99 I
D7U 19 7 8.14 4.31 U
D14I 4 14 15.63 9.22 I
D14U 4 14 15.63 8.31 U
D17I 3 17 19.15 8.27 I
D17U 3 17 19.15 7.25 U
D21I 4 21 23.23 9.01 I
D21U 4 21 23.23 7.83 U
D24I 3 24 26.60 8.22 I
D24U 3 24 26.60 6.58 U
D28I 4 28 30.61 8.83 I
D28U 4 28 30.61 7.37 U