Rv1956 Possible transcriptional regulatory protein

Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv1956 higA Possible transcriptional regulatory protein CDS 2202138 2202587 + 450 149 TRUE

Rv1956 (Possible transcriptional regulatory protein) is predicted to be co-regulated in modules bicluster_0018 with residual 0.62 and bicluster_0090 with residual 0.37.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.55 and 25.00 for bicluster_0018 and 1,600.00 and 1,700.00 for bicluster_0090 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 22
Gene Target Differential Expression Distance Expression pvalue Type
Aldehyde dehydrogenase (EC
No -52 -0.01 0.95267 Primary.TSS
Fatty acid desaturase occurring in virulence cluster
No -2 -0.43 0.207005 Primary.TSS
Acetyl-coenzyme A carboxyl transferase alpha chain (EC / Acetyl-coenzyme A carboxyl transferase beta chain (EC
No 15 -0.01 0.97685 CDS
Enoyl-CoA hydratase (EC
No -12 -0.42 0.110022 Primary.TSS
No -107 -0.11 0.743876 Primary.TSS
Mobile element protein
No 62 -0.19 0.33333 Primary.TSS
No 16 0.54 0.24357 Internal.TSS
Universal stress protein UspA and related nucleotide-binding proteins
No 0 -0.2 0.463089 Primary.TSS
Putative ferredoxin
No -127 0.35 0.377505 CDS
Magnesium and cobalt efflux protein CorC
No -108 0.13 0.405712 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
Operon # Operon
1281 -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics


Not assigned Not assigned
Locus Tuberculist Genome View


Locus Tag KEGG Pathways


not assigned to any KEGG Pathway.
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network


GI Number Protein ID Blast Conserved Domains
15609093 NP_216472.1 Run

response to hypoxia

response to hypoxia

Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
GO Category: 
Total items in this category:  

negative regulation of growth

negative regulation of growth

Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism.
GO Category: 
Total items in this category:  

positive regulation of growth

positive regulation of growth

Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism.
GO Category: 
Total items in this category:  
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 GSM1426746 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426747 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426748 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426749 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426750 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1956_B186 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.080000 0.75

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: 0.0266518
p-value INH: 0.910292
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D24U 3 24 26.60 13.09 U
D17U 3 17 19.15 13.16 U
D28U 4 28 30.61 13.18 U
D24I 3 24 26.60 13.23 I
D28I 4 28 30.61 13.34 I
D21U 4 21 23.23 13.44 U
D14U 4 14 15.63 13.52 U
D17I 3 17 19.15 13.64 I
D5U 17 5 6.00 13.64 U
D21I 4 21 23.23 13.70 I
D5I 9 5 6.00 13.82 I
D7U 19 7 8.14 13.85 U
D3U 3 3 3.83 13.97 U
D3I 3 3 3.83 13.97 I
D14I 4 14 15.63 13.98 I
D0U 27 0 0.00 14.12 U
D7I 18 7 8.14 14.26 I