Detailed view for TGME49_264670

Basic information

TDR Targets ID: 262347
Toxoplasma gondii, DNA polymerase family B protein
Source Database / ID:  ToxoDB 

pI: 8.3198 | Length (AA): 4257 | MW (Da): 457329 | 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

PF00136   DNA polymerase family B

Gene Ontology

Mouse over links to read term descriptions.
GO:0019985   bypass DNA synthesis  
GO:0016035   zeta DNA polymerase complex  
GO:0003887   DNA-directed DNA polymerase activity  
GO:0003677   DNA binding  
GO:0003676   nucleic acid binding  
GO:0000166   nucleotide binding  
GO:0006281   DNA repair  
GO:0006260   DNA replication  

Metabolic Pathways

Global map (KEGG)

Structural information

Modbase 3D models:

There are 7 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
374 456 2khm (A) 29 114 42.00 0.0015 0.08 0.321197 0.72
911 1053 4lsw (A) 107 258 33.00 0.96 0.63 0.103292 0.89
1191 1267 5fuc (C) 116 199 39.00 0.43 0.28 0.275788 0.36
2772 3767 3iay (A) 99 984 16.00 0 1 0.117368 1.45
2824 3933 5exr (C) 375 1391 14.00 0 0.8 0.008147 1.81
3265 3599 5mdn (A) 373 607 36.00 0.0000000017 1 -0.0106061 0.85
3301 3607 2gv9 (A) 701 951 35.00 0 1 -0.0281835 0.86

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 Bradyzoite. Gregory Sibley/Greg
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile ME49 merozoite. Hehl AB
Show/Hide expression data references
  • Sibley/Greg ToxoDB
  • Gregory ToxoDB
  • Fritz HM Transcriptomic analysis of toxoplasma development reveals many novel functions and structures specific to sporozoites and oocysts.
  • 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.

Orthologs

Ortholog group members (OG5_128651)

Species Accession Gene Product
Arabidopsis thaliana AT1G67500   DNA polymerase zeta subunit
Arabidopsis thaliana AT1G55040   Zn-finger in Ran binding domain-containing protein
Babesia bovis BBOV_III010120   DNA polymerase family B family protein
Brugia malayi Bm1_09315   DNA polymerase family B containing protein
Candida albicans CaO19.7389   similar to N terminus of S. cerevisiae REV3 (YPL167C) DNA polymerase zeta subunit involved in DNA repair
Candida albicans CaO19.7390   similar to C terminus of S. cerevisiae REV3 (YPL167C) DNA polymerase zeta subunit involved in DNA repair
Caenorhabditis elegans CELE_Y37B11A.2   Protein Y37B11A.2
Dictyostelium discoideum DDB_G0271608   DNA polymerase zeta catalytic subunit
Drosophila melanogaster Dmel_CG1925   mutagen-sensitive 205
Echinococcus granulosus EgrG_000149300   DNA polymerase zeta catalytic subunit
Entamoeba histolytica EHI_068010   DNA polymerase zeta catalytic subunit, putative
Echinococcus multilocularis EmuJ_000149300   DNA polymerase zeta catalytic subunit
Homo sapiens ENSG00000009413   REV3-like, polymerase (DNA directed), zeta, catalytic subunit
Leishmania braziliensis LbrM.23.1450   DNA polymerase zeta catalytic subunit, putative
Leishmania donovani LdBPK_231590.1   DNA polymerase zeta catalytic subunit, putative
Leishmania infantum LinJ.23.1590   DNA polymerase zeta catalytic subunit, putative
Leishmania major LmjF.23.1330   DNA polymerase zeta catalytic subunit, putative
Leishmania mexicana LmxM.23.1330   DNA polymerase zeta catalytic subunit, putative
Loa Loa (eye worm) LOAG_13925   hypothetical protein
Loa Loa (eye worm) LOAG_14745   hypothetical protein
Loa Loa (eye worm) LOAG_11287   hypothetical protein
Loa Loa (eye worm) LOAG_12098   hypothetical protein
Mus musculus ENSMUSG00000019841   REV3-like, catalytic subunit of DNA polymerase zeta RAD54 like (S. cerevisiae)
Neospora caninum NCLIV_040490   DNA polymerase (EC 2.7.7.7), related
Oryza sativa 4342984   Os07g0404300
Onchocerca volvulus OVOC2477   DNA polymerase homolog
Saccharomyces cerevisiae YPL167C   Rev3p
Schistosoma japonicum Sjp_0210840   ko:K02350 DNA polymerase zeta subunit, putative
Schistosoma japonicum Sjp_0210830   expressed protein
Schistosoma mansoni Smp_125680   DNA polymerase zeta catalytic subunit
Schmidtea mediterranea mk4.001967.04  
Schmidtea mediterranea mk4.001967.03   DNA polymerase
Schmidtea mediterranea mk4.001967.02   DNA polymerase
Trypanosoma brucei gambiense Tbg972.8.3050   DNA polymerase zeta catalytic subunit, putative
Trypanosoma brucei Tb927.8.3290   DNA polymerase zeta catalytic subunit, putative
Trypanosoma congolense TcIL3000_8_3340   DNA polymerase zeta catalytic subunit, putative
Trypanosoma cruzi TcCLB.509769.130   DNA polymerase zeta catalytic subunit, putative
Toxoplasma gondii TGME49_264670   DNA polymerase family B protein
Trichomonas vaginalis TVAG_328140   DNA polymerase alpha catalytic subunit, putative

Essentiality

TGME49_264670 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.3290 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.8.3290 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.8.3290 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.8.3290 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
TGME49_264670 this record Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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

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

Druggability index (range: 0 to 1): 0.5

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.

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Gene identifier TGME49_264670 (Toxoplasma gondii), DNA polymerase family B protein
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