Rv2986c DNA-binding protein HU / low-complexity, AKP-rich domain

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv2986c hupB DNA-binding protein HU / low-complexity, AKP-rich domain CDS 3343176 3343820 - 645 214 FALSE

Rv2986c (DNA-binding protein HU / low-complexity, AKP-rich domain) is predicted to be co-regulated in modules bicluster_0316 with residual 0.52 and bicluster_0503 with residual 0.54.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.49 and 70.00 for bicluster_0316 and 2.50 and 5,400.00 for bicluster_0503 respectively.

These modules are enriched for following go terms: nucleotide biosynthetic process, nucleoside phosphate biosynthetic proces..., nucleotide metabolic process, hydroxymethyl-, formyl- and related tran... .

This gene is found to be for growth on cholesterol.

Mutant available?:

Product (LegacyBRC) Product (RefSeq)
DNA-binding protein HU homolog DNA-binding protein HU
Operon # Operon
1949
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
15610123 NP_217502.1 Run
GO:0003677

DNA binding

DNA binding

Details: 
Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid).
GO Category: 
molecular_function
37
Total items in this category:  
GO:0005515

protein binding

protein binding

Details: 
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
GO Category: 
molecular_function
135
Total items in this category:  
GO:0005618

cell wall

cell wall

Details: 
The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan.
GO Category: 
cellular_component
320
Total items in this category:  
GO:0005886

plasma membrane

plasma membrane

Details: 
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO Category: 
cellular_component
1284
Total items in this category:  
GO:0010106

cellular response to iron ion starvation

cellular response to iron ion starvation

Details: 
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of iron ions.
GO Category: 
biological_process
14
Total items in this category:  
GO:0040007

growth

growth

Details: 
The increase in size or mass of an entire organism, a part of an organism or a cell.
GO Category: 
biological_process
621
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 GSM1426889 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426890 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426891 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2986c_B630 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
NA NA

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: 0.000354572
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 14.09 U
D3I 3 3 3.83 13.85 I
D3U 3 3 3.83 13.66 U
D5I 9 5 6.00 14.33 I
D5U 17 5 6.00 13.85 U
D7I 18 7 8.14 14.66 I
D7U 19 7 8.14 14.29 U
D14I 4 14 15.63 15.66 I
D14U 4 14 15.63 14.36 U
D17I 3 17 19.15 16.77 I
D17U 3 17 19.15 14.39 U
D21I 4 21 23.23 16.04 I
D21U 4 21 23.23 14.34 U
D24I 3 24 26.60 16.99 I
D24U 3 24 26.60 14.33 U
D28I 4 28 30.61 15.90 I
D28U 4 28 30.61 13.99 U