Detailed view for TGME49_293460

Basic information

TDR Targets ID: 263277
Toxoplasma gondii, ATP-dependent DNA ligase domain-containing protein
Source Database / ID:  ToxoDB 

pI: 7.9097 | Length (AA): 1385 | MW (Da): 151347 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG5

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF01068   ATP dependent DNA ligase domain
PF04675   DNA ligase N terminus
PF04679   ATP dependent DNA ligase C terminal region

Gene Ontology

Mouse over links to read term descriptions.
GO:0003910   DNA ligase (ATP) activity  
GO:0051103   DNA ligation during DNA repair  
GO:0005622   intracellular  
GO:0005524   ATP binding  
GO:0003677   DNA binding  
GO:0006310   DNA recombination  
GO:0006281   DNA repair  
GO:0006260   DNA replication  

Metabolic Pathways

Non-homologous end-joining (KEGG)

Structural information

Modbase 3D models:

There are 6 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
6 751 1x9n (A) 275 900 22.00 0 1 0.422728 1.4
16 747 3w1b (A) 12 601 30.00 0 1 0.49392 0.83
20 741 3w1b (A) 16 595 33.00 0 1 0.495 1.16
873 988 2d8m (A) 14 127 15.00 0 0.71 0.320155 -0.55
879 938 2ebu (A) 404 462 27.00 0 0.72 0.361721 -0.15
1140 1215 2jw5 (A) 50 126 7.00 0.0051 0 0.0679736 0.31

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

No structure availble in the PDB for this protein

Expression

Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile ME49 Oocyst. Fritz HM
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile VEG Tachyzoite, ME49 Tachyzoite, ME49 merozoite, ME49 Bradyzoite. Gregory Hehl AB Sibley/Greg
Show/Hide expression data references
  • Hehl AB Asexual expansion of Toxoplasma gondii merozoites is distinct from tachyzoites and entails expression of non-overlapping gene families to attach, invade, and replicate within feline enterocytes.
  • Fritz HM Transcriptomic analysis of toxoplasma development reveals many novel functions and structures specific to sporozoites and oocysts.
  • Gregory ToxoDB
  • Sibley/Greg ToxoDB

Orthologs

Ortholog group members (OG5_130132)

Species Accession Gene Product
Arabidopsis thaliana AT5G57160   DNA ligase 4
Brugia malayi Bm1_09010   ATP dependent DNA ligase C terminal region family protein
Candida albicans CaO19.5798   ATP-dependent DNA ligase implicated in dsDNA break repair via nonhomologous end-joining
Candida albicans CaO19.13220   ATP-dependent DNA ligase implicated in dsDNA break repair via nonhomologous end-joining
Caenorhabditis elegans CELE_C07H6.1   Protein LIG-4
Dictyostelium discoideum DDB_G0292760   BRCT domain-containing protein
Drosophila melanogaster Dmel_CG12176   Ligase4
Echinococcus granulosus EgrG_000257800   dna ligase 4
Echinococcus multilocularis EmuJ_000257800   dna ligase 4
Homo sapiens ENSG00000174405   ligase IV, DNA, ATP-dependent
Loa Loa (eye worm) LOAG_05773   hypothetical protein
Mus musculus ENSMUSG00000049717   ligase IV, DNA, ATP-dependent
Neospora caninum NCLIV_000420   DNA ligase, putative
Saccharomyces cerevisiae YOR005C   DNA ligase (ATP) DNL4
Schistosoma japonicum Sjp_0010480   ko:K10777 DNA ligase 4, putative
Schistosoma japonicum Sjp_0201790   DNA ligase 4, putative
Schistosoma mansoni Smp_148660   DNA ligase IV
Schmidtea mediterranea mk4.006311.00   DNA ligase 4
Schmidtea mediterranea mk4.000087.08  
Toxoplasma gondii TGME49_293460   ATP-dependent DNA ligase domain-containing protein

Essentiality

TGME49_293460 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
CELE_C07H6.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_C07H6.1 Caenorhabditis elegans slow growth wormbase
TGME49_293460 this record Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.

In any case, if you have information about papers containing relevant validation data for this target, please contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

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Gene identifier TGME49_293460 (Toxoplasma gondii), ATP-dependent DNA ligase domain-containing protein
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