Rv0938 ATP-dependent DNA ligase (EC 6.5.1.1) clustered with Ku protein, LigD

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0938 ligD ATP-dependent DNA ligase (EC 6.5.1.1) clustered with Ku protein, LigD CDS 1046136 1048415 + 2 280 759 FALSE

Rv0938 (ATP-dependent DNA ligase (EC 6.5.1.1) clustered with Ku protein, LigD) is predicted to be co-regulated in modules bicluster_0388 with residual 0.53 and bicluster_0397 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.05 for bicluster_0388 and 0.00 and 0.00 for bicluster_0397 respectively.

These modules are enriched for following go terms: nitrogen compound metabolic process, carbon-oxygen lyase activity.

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 10/16/2017 - 08:59
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-15037 MT0965 1213
Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No -36 -0.56 0.0717121 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0388
e.value: 
0.000000055
Motif Bicluster: 
e.value: 
0.047
Motif Bicluster: 
0.53
bicluster_0397
e.value: 
0.000000000016
Motif Bicluster: 
e.value: 
0.000063
Motif Bicluster: 
0.58
Product (LegacyBRC) Product (RefSeq)
Putative DNA ligase-like protein Rv0938_MT0965 ATP-dependent DNA ligase
Operon # Operon
625 -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Base excision repair

17
Total items in this category:  

KEGG

Nucleotide excision repair

14
Total items in this category:  

KEGG

Mismatch repair

19
Total items in this category:  

KEGG

Non-homologous end-joining

5
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15608078 NP_215453.1 Run
GO:0000287

magnesium ion binding

magnesium ion binding

Details: 
Interacting selectively and non-covalently with magnesium (Mg) ions.
GO Category: 
molecular_function
52
Total items in this category:  
GO:0003887

DNA-directed DNA polymerase activity

DNA-directed DNA polymerase activity

Details: 
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and primer.
GO Category: 
molecular_function
8
Total items in this category:  
GO:0003896

DNA primase activity

DNA primase activity

Details: 
Catalysis of the synthesis of a short RNA primer on a DNA template, providing a free 3'-OH that can be extended by DNA-directed DNA polymerases. Catalyzed by a DNA-directed RNA polymerase that forms a complex with alpha DNA polymerase.
GO Category: 
molecular_function
2
Total items in this category:  
GO:0003899

DNA-directed RNA polymerase activity

DNA-directed RNA polymerase activity

Details: 
Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
GO Category: 
molecular_function
5
Total items in this category:  
GO:0003909

DNA ligase activity

DNA ligase activity

Details: 
Catalysis of the formation of a phosphodiester bond between the 3'-hydroxyl group at the end of one DNA chain and the 5'-phosphate group at the end of another. This reaction requires an energy source such as ATP or NAD+.
GO Category: 
molecular_function
2
Total items in this category:  
GO:0003910

DNA ligase (ATP) activity

DNA ligase (ATP) activity

Details: 
Catalysis of the reaction: ATP + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + diphosphate + deoxyribonucleotide(n+m).
GO Category: 
molecular_function
3
Total items in this category:  
GO:0004652

polynucleotide adenylyltransferase activity

polynucleotide adenylyltransferase activity

Details: 
Catalysis of the template-independent extension of the 3'- end of an RNA or DNA strand by addition of one adenosine molecule at a time. Cannot initiate a chain 'de novo'. The primer, depending on the source of the enzyme, may be an RNA or DNA fragment, or oligo(A) bearing a 3'-OH terminal group.
GO Category: 
molecular_function
1
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:0005524

ATP binding

ATP binding

Details: 
Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO Category: 
molecular_function
58
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:  
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.
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.210000 2.84

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:
p-value INH: