Rv2478c Single-strand DNA binding protein

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv2478c Single-strand DNA binding protein CDS 2784123 2784608 - 486 161 FALSE

Rv2478c (Single-strand DNA binding protein) is predicted to be co-regulated in modules bicluster_0130 with residual 0.52 and bicluster_0597 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 130.00 and 570.00 for bicluster_0130 and 0.00 and 0.28 for bicluster_0597 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Product (LegacyBRC) Product (RefSeq)
Single-stranded DNA-binding protein
Operon # Operon
1634
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

DNA replication

14
Total items in this category:  

KEGG

Mismatch repair

19
Total items in this category:  

KEGG

Homologous recombination

22
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15609615 NP_216994.1 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 GSM1426827 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426828 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426829 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2478c_B621 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.760000 1.67

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: 0.0151102
p-value INH: 0.885314
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 14.54 U
D3I 3 3 3.83 15.01 I
D3U 3 3 3.83 15.15 U
D5I 9 5 6.00 15.06 I
D5U 17 5 6.00 14.79 U
D7I 18 7 8.14 15.75 I
D7U 19 7 8.14 15.74 U
D14I 4 14 15.63 17.32 I
D14U 4 14 15.63 17.07 U
D17I 3 17 19.15 17.71 I
D17U 3 17 19.15 17.69 U
D21I 4 21 23.23 17.37 I
D21U 4 21 23.23 17.67 U
D24I 3 24 26.60 17.67 I
D24U 3 24 26.60 18.40 U
D28I 4 28 30.61 17.23 I
D28U 4 28 30.61 18.48 U