Rv2017 Zn peptidase with DNA binding

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv2017 Zn peptidase with DNA binding CDS 2263998 2265038 + 1 041 346 TRUE

Rv2017 (Zn peptidase with DNA binding) is predicted to be co-regulated in modules bicluster_0346 with residual 0.51 and bicluster_0434 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.14 for bicluster_0346 and 0.00 and 0.00 for bicluster_0434 respectively.

These modules are enriched for following go terms: cellular macromolecule catabolic process, cellular protein metabolic process, coenzyme biosynthetic process, cofactor biosynthetic process.

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
Repressed 1 -2.8 1.65e-16 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
1324 -
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
15609154 NP_216533.1 Run
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 GSM1426777 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426778 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426779 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2017_B613 UCSC Browser Tracks
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: 0.0645359
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D24I 3 24 26.60 6.67 I
D28I 4 28 30.61 6.86 I
D17I 3 17 19.15 7.63 I
D21I 4 21 23.23 7.89 I
D24U 3 24 26.60 8.21 U
D14I 4 14 15.63 8.48 I
D17U 3 17 19.15 8.52 U
D28U 4 28 30.61 8.69 U
D21U 4 21 23.23 8.70 U
D14U 4 14 15.63 8.86 U
D7U 19 7 8.14 9.87 U
D3U 3 3 3.83 10.46 U
D3I 3 3 3.83 10.53 I
D0U 27 0 0.00 10.61 U
D7I 18 7 8.14 10.68 I
D5U 17 5 6.00 12.93 U
D5I 9 5 6.00 13.07 I