Rv0054 Single-stranded DNA-binding protein

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0054 ssb Single-stranded DNA-binding protein CDS 58586 59080 + 495 164 TRUE

Rv0054 (Single-stranded DNA-binding protein) is predicted to be co-regulated in modules bicluster_0247 with residual 0.41 and bicluster_0445 with residual 0.34.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 430.00 and 9,100.00 for bicluster_0247 and 920.00 and 3,100.00 for bicluster_0445 respectively.

These modules are enriched for following go terms: phosphorus-oxygen lyase activity.

This gene is found to be non-essential for growth on cholesterol.

Mutant available?:

Displaying 1 - 4 of 4
Gene Target Differential Expression Distance Expression pvalue Type
No -61 0.32 0.985283 Primary.TSS
Translation initiation factor 1
No -44 0.16 0.987861 Primary.TSS
Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases
No -140 -0.01 0.999165 CDS
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60)
No -132 0 0.999214 Primary.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, MarR family
No -9 0.16 0.818339 CDS
Motif 1 Motif 2 Residual
bicluster_0247
e.value: 
430
Motif Bicluster: 
e.value: 
9100
Motif Bicluster: 
0.41
bicluster_0445
e.value: 
920
Motif Bicluster: 
e.value: 
3100
Motif Bicluster: 
0.34
Product (LegacyBRC) Product (RefSeq)
Single-stranded DNA-binding protein single-stranded DNA-binding protein
Operon # Operon
36 Rv0054
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
15607196 NP_214568.1 Run
GO:0003697

single-stranded DNA binding

single-stranded DNA binding

Details: 
Interacting selectively and non-covalently with single-stranded DNA.
GO Category: 
molecular_function
2
Total items in this category:  
GO:0003697

single-stranded DNA binding

single-stranded DNA binding

Details: 
Interacting selectively and non-covalently with single-stranded DNA.
GO Category: 
molecular_function
2
Total items in this category:  
GO:0005576

extracellular region

extracellular region

Details: 
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
GO Category: 
cellular_component
272
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:0006974

response to DNA damage stimulus

response to DNA damage stimulus

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 a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
GO Category: 
biological_process
8
Total items in this category:  
GO:0051289

protein homotetramerization

protein homotetramerization

Details: 
The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
GO Category: 
biological_process
17
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 GSM1426390 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426391 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426392 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0054_B605 UCSC Browser Tracks
Quantitative Proteomics Data
Cholesterol Essentiality t-test p-value Cholesterol/Glycerol Ratio
non-essential 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.

Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.80 U
D3I 3 3 3.83 13.71 I
D3U 3 3 3.83 13.85 U
D5I 9 5 6.00 12.40 I
D5U 17 5 6.00 13.04 U
D7I 18 7 8.14 12.15 I
D7U 19 7 8.14 13.65 U
D14I 4 14 15.63 7.43 I
D14U 4 14 15.63 13.70 U
D17I 3 17 19.15 4.42 I
D17U 3 17 19.15 13.80 U
D21I 4 21 23.23 3.99 I
D21U 4 21 23.23 13.45 U
D24I 3 24 26.60 2.33 I
D24U 3 24 26.60 13.62 U
D28I 4 28 30.61 4.59 I
D28U 4 28 30.61 13.07 U