Rv3840 Cell envelope-associated transcriptional attenuator LytR-CpsA-Psr, subfamily A1 (as in PMID19099556)

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv3840 Cell envelope-associated transcriptional attenuator LytR-CpsA-Psr, subfamily A1 (as in PMID19099556) CDS 4313567 4313980 + 414 137 FALSE

Rv3840 (Cell envelope-associated transcriptional attenuator LytR-CpsA-Psr, subfamily A1 (as in PMID19099556)) is predicted to be co-regulated in modules bicluster_0059 with residual 0.54 and bicluster_0107 with residual 0.57.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.07 and 75.00 for bicluster_0059 and 3.30 and 320.00 for bicluster_0107 respectively.

These modules are enriched for following go terms: pigment metabolic process, pigment biosynthetic process .

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 New Primary UTR Primary TSS Re-Annotated Start Tuberculist Annotated Start
-0.51 43 4313610 8 446 4313172 4313618 4313567
Last update: 11/20/2020 - 12:12
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-18850 MT3948 3165
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
2512 -
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
15610976 NP_218357.1 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 GSM1427044 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427045 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427046 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3840_B227 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.710000 1.29

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: 0.00133119
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.00 U
D3I 3 3 3.83 12.77 I
D3U 3 3 3.83 12.35 U
D5I 9 5 6.00 13.11 I
D5U 17 5 6.00 12.71 U
D7I 18 7 8.14 13.22 I
D7U 19 7 8.14 12.77 U
D14I 4 14 15.63 12.69 I
D14U 4 14 15.63 11.77 U
D17I 3 17 19.15 12.63 I
D17U 3 17 19.15 11.32 U
D21I 4 21 23.23 12.64 I
D21U 4 21 23.23 11.43 U
D24I 3 24 26.60 12.21 I
D24U 3 24 26.60 10.74 U
D28I 4 28 30.61 12.32 I
D28U 4 28 30.61 10.57 U