Rv3549c Probable short-chain type dehydrogenase/reductase (EC 1.-.-.-)

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv3549c Probable short-chain type dehydrogenase/reductase (EC 1.-.-.-) CDS 3988319 3989098 - 780 259 FALSE

Rv3549c (Probable short-chain type dehydrogenase/reductase (EC 1.-.-.-)) is predicted to be co-regulated in modules bicluster_0152 with residual 0.50 and bicluster_0181 with residual 0.51.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.09 for bicluster_0152 and 0.00 and 88.00 for bicluster_0181 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

Last update: 10/16/2017 - 15:33
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-15024 MT3653 1186
Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional factor in putative operon for degradation of branched-chain alkanes, nitroalkanes and may be also cyclic ketones, alkenoic acids
Repressed 21 -2.46 0.00000000000807 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0152
e.value: 
0.00000000028
Motif Bicluster: 
e.value: 
0.094
Motif Bicluster: 
0.50
bicluster_0181
e.value: 
0.000000000000033
Motif Bicluster: 
e.value: 
88
Motif Bicluster: 
0.51
Product (LegacyBRC) Product (RefSeq)
PROBABLE SHORT-CHAIN TYPE DEHYDROGENASE_REDUCTASE short chain dehydrogenase
Operon # Operon
2315 -
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
15610685 NP_218066.1 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.
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.000000 0.00

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: