Rv0038

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0038 CDS 41304 41912 + 609 202 FALSE

Rv0038 () is predicted to be co-regulated in modules bicluster_0329 with residual 0.54 and bicluster_0464 with residual 0.52.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 1.10 for bicluster_0329 and 0.03 and 2.20 for bicluster_0464 respectively.

These modules are enriched for following go terms: inositol metabolic process, inositol biosynthetic process, polyol biosynthetic process, acyl-CoA dehydrogenase activity .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

BASS Score Distance to Tuberculist Start Codon Internal TSS New Internal UTR Primary TSS Re-Annotated Start Tuberculist Annotated Start
-0.581 81 41385 -78 41307 41307 41304
Last update: 10/16/2017 - 16:54
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-14761 MT0043 85
Product (LegacyBRC) Product (RefSeq)
UPF0301 protein Rv0038_MT0043
Operon # Operon
23
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics
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
15607180 NP_214552.1 Run
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:  
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 GSM1426377 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426378 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426379 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426380 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0038_B347 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.440000 1.67

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 3.30 U
D3I 3 3 3.83 3.57 I
D3U 3 3 3.83 4.06 U
D5I 9 5 6.00 I
D5U 17 5 6.00 U
D7I 18 7 8.14 3.25 I
D7U 19 7 8.14 3.61 U
D14I 4 14 15.63 3.64 I
D14U 4 14 15.63 3.08 U
D17I 3 17 19.15 4.22 I
D17U 3 17 19.15 2.99 U
D21I 4 21 23.23 3.82 I
D21U 4 21 23.23 3.62 U
D24I 3 24 26.60 4.53 I
D24U 3 24 26.60 2.97 U
D28I 4 28 30.61 3.88 I
D28U 4 28 30.61 2.97 U