Rv3830c Beta-carotene ketolase (EC 1.14.-.-)

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv3830c Beta-carotene ketolase (EC 1.14.-.-) CDS 4305056 4305685 - 630 209 TRUE

Rv3830c (Beta-carotene ketolase (EC 1.14.-.-)) is predicted to be co-regulated in modules bicluster_0027 with residual 0.56 and bicluster_0178 with residual 0.53.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.04 for bicluster_0027 and 140.00 and 36,000.00 for bicluster_0178 respectively.

These modules are enriched for following go terms: disaccharide metabolic process, trehalose metabolic process, trehalose biosynthetic process, disaccharide biosynthetic process, carbohydrate biosynthetic process .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 11/20/2020 - 12:12
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-13626 MT3938 1056
Displaying 1 - 10 of 71
Gene Target Differential Expression Distance Expression pvalue Type
Transcriptional regulator, MarR family
No 18 0.15 0.999473 CDS
Predicted cobalt transporter in Mycobacteria
No 63 0.04 0.999473 Primary.TSS
No 63 -0.51 0.999473 Antisense.TSS
No 47 -0.51 0.999473 Internal.TSS
Possible membrane protein
No -21 0.34 0.999473 Internal.TSS
Possible membrane protein
No -31 0.34 0.999473 Antisense.TSS
Possible membrane protein
No -47 0.34 0.999473 CDS
Pyrrolidone-carboxylate peptidase (EC 3.4.19.3)
No -31 0.13 0.999473 Primary.TSS
Carboxylate-amine ligase
No -105 0.02 0.999473 CDS
Isocitrate lyase (EC 4.1.3.1) / Methylisocitrate lyase (EC 4.1.3.30)
No -23 -0.02 0.999473 Primary.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
No results were found
Motif 1 Motif 2 Residual
bicluster_0027
e.value: 
0.0000000000000019
Motif Bicluster: 
e.value: 
0.036
Motif Bicluster: 
0.56
bicluster_0178
e.value: 
140
Motif Bicluster: 
e.value: 
36000
Motif Bicluster: 
0.53
Product (LegacyBRC) Product (RefSeq)
TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY TETR-FAMILY] transcriptional regulatory protein TetR-family
Operon # Operon
2505
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
15610966 NP_218347.1 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 GSM1427038 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427039 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427040 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3830c_B380 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.710000 0.61

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: 0.0586623
p-value INH: 0.832328
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.22 U
D3I 3 3 3.83 11.92 I
D3U 3 3 3.83 11.28 U
D5I 9 5 6.00 12.82 I
D5U 17 5 6.00 12.57 U
D7I 18 7 8.14 12.18 I
D7U 19 7 8.14 11.54 U
D14I 4 14 15.63 10.27 I
D14U 4 14 15.63 10.14 U
D17I 3 17 19.15 9.54 I
D17U 3 17 19.15 9.72 U
D21I 4 21 23.23 9.51 I
D21U 4 21 23.23 9.72 U
D24I 3 24 26.60 8.36 I
D24U 3 24 26.60 9.03 U
D28I 4 28 30.61 8.68 I
D28U 4 28 30.61 9.22 U