Rv3557c Transcriptional factor in putative operon for degradation of branched-chain alkanes, nitroalkanes and may be also cyclic ketones, alkenoic acids

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv3557c Transcriptional factor in putative operon for degradation of branched-chain alkanes, nitroalkanes... CDS 3997029 3997631 - 603 200 TRUE

Rv3557c (Transcriptional factor in putative operon for degradation of branched-chain alkanes, nitroalkanes and may be also cyclic ketones, alkenoic acids) is predicted to be co-regulated in modules bicluster_0181 with residual 0.51 and bicluster_0457 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 88.00 for bicluster_0181 and 2,200.00 and 4,000.00 for bicluster_0457 respectively.

These modules are enriched for following go terms: oxidoreductase activity, acting on the C..., flavin adenine dinucleotide binding .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

BASS Score New Primary UTR Primary TSS Re-Annotated Start Tuberculist Annotated Start
-0.848 279 3997901 3997622 3997631
Last update: 11/20/2020 - 12:12
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-15087 MT3661 1798
Displaying 1 - 10 of 14
Gene Target Differential Expression Distance Expression pvalue Type
Possible conserved exported protein
No -28 0.22 0.766969 CDS
Induced -64 0.59 0.0027519 CDS
No -28 -0.46 0.509178 CDS
Probable phiRV1 phage protein
No -44 0.12 0.893668 CDS
FIG055075: Possibly a cell division protein, antigen 84 in Mycobacteria
No 66 0.13 0.593201 Primary.TSS
No 0 0.23 0.759181 Internal.TSS
No -26 0.23 0.759181 CDS
No -32 0.03 0.96964 Primary.TSS
DNA-binding protein, CopG family
No -56 -0.59 0.280619 CDS
DNA-binding protein, CopG family
No -32 -0.59 0.280619 Internal.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, AsnC family
No 44 0.03 0.991204 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY TETR-FAMILY] TetR family transcriptional regulator
Operon # Operon
2320
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
15610693 NP_218074.1 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 GSM1427005 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427006 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427007 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427005 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427006 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427007 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3557c_B457 UCSC Browser Tracks
Rv3557c_B639 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.030000 0.95

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: 0.00287156
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.16 U
D3I 3 3 3.83 13.65 I
D3U 3 3 3.83 13.50 U
D5I 9 5 6.00 13.96 I
D5U 17 5 6.00 13.63 U
D7I 18 7 8.14 13.72 I
D7U 19 7 8.14 12.65 U
D14I 4 14 15.63 12.61 I
D14U 4 14 15.63 11.34 U
D17I 3 17 19.15 12.17 I
D17U 3 17 19.15 10.56 U
D21I 4 21 23.23 12.11 I
D21U 4 21 23.23 10.99 U
D24I 3 24 26.60 11.60 I
D24U 3 24 26.60 10.20 U
D28I 4 28 30.61 11.56 I
D28U 4 28 30.61 10.44 U