Rv2887 Transcriptional regulator, MarR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv2887 Transcriptional regulator, MarR family CDS 3196431 3196850 + 420 139 TRUE

Rv2887 (Transcriptional regulator, MarR family) is predicted to be co-regulated in modules bicluster_0140 with residual 0.62 and bicluster_0180 with residual 0.54.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.00 for bicluster_0140 and 19,000.00 and 20,000.00 for bicluster_0180 respectively.

These modules are enriched for following go terms: cellular macromolecule biosynthetic proc..., macromolecule biosynthetic process, regulation of transcription, DNA-depende..., regulation of RNA metabolic process, regulation of RNA biosynthetic process, regulation of biosynthetic process, regulation of gene expression, regulation of macromolecule biosynthetic..., regulation of cellular biosynthetic proc..., regulation of cellular macromolecule bio..., regulation of nucleobase-containing comp..., regulation of nitrogen compound metaboli..., regulation of cellular metabolic process, regulation of macromolecule metabolic pr..., regulation of primary metabolic process, transcription, DNA-dependent, regulation of metabolic process, RNA biosynthetic process, nucleic acid metabolic process, nucleic acid binding transcription facto..., sequence-specific DNA binding transcript....

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 39
Gene Target Differential Expression Distance Expression pvalue Type
Iron-regulated heparin binding hemagglutinin HbhA (Adhesin)
No -24 -0.12 0.586282 CDS
LSU ribosomal protein L15p (L27Ae)
No -63 0.22 0.414542 Internal.TSS
Possible protease IV SppA (endopeptidase IV) (signal peptide peptidase)
No -63 -0.02 0.92843 Primary.TSS
Fatty acid desaturase occurring in virulence cluster
No -43 0.31 0.452262 Primary.TSS
No -71 -0.3 0.328342 CDS
Transcriptional regulator, XRE family
No -136 -0.61 0.176202 CDS
Lysine decarboxylase family
No -1 -0.33 0.18152 Antisense.TSS
Methyltransferase
No -99 -0.27 0.562428 Primary.TSS
O-antigen acetylase
Repressed -15 -1.15 1.02e-22 Primary.TSS
Transcriptional repressor Mce3R, TetR family
Repressed 35 -0.84 0.00960828 Primary.TSS
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, MarR family
Induced -8 2.81 8.46e-34 Primary.TSS
Transcriptional regulator, TetR family
Repressed 0 -0.8 0.0000483 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0140
e.value: 
0.0000061
Motif Bicluster: 
e.value: 
0.000019
Motif Bicluster: 
0.62
bicluster_0180
e.value: 
19000
Motif Bicluster: 
e.value: 
20000
Motif Bicluster: 
0.54
Product (LegacyBRC) Product (RefSeq)
Uncharacterized HTH-type transcriptional regulator Rv2887_MT2955 transcriptional regulatory protein
Operon # Operon
1887
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
15610024 NP_217403.1 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 GSM1426883 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426884 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426885 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2887_B137 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.090000 0.16

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: 0.125073
p-value INH: 0.900603
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.44 U
D3I 3 3 3.83 13.50 I
D3U 3 3 3.83 13.28 U
D5I 9 5 6.00 12.15 I
D5U 17 5 6.00 12.35 U
D7I 18 7 8.14 12.81 I
D7U 19 7 8.14 12.90 U
D14I 4 14 15.63 10.02 I
D14U 4 14 15.63 12.38 U
D17I 3 17 19.15 8.35 I
D17U 3 17 19.15 12.14 U
D21I 4 21 23.23 7.55 I
D21U 4 21 23.23 12.04 U
D24I 3 24 26.60 4.62 I
D24U 3 24 26.60 11.78 U
D28I 4 28 30.61 5.23 I
D28U 4 28 30.61 11.61 U