Detailed view for TGME49_305310

Basic information

TDR Targets ID: 260403
Toxoplasma gondii, ERCC4 domain-containing protein
Source Database / ID:  ToxoDB 

pI: 7.4489 | Length (AA): 2053 | MW (Da): 223461 | 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

PF02732   ERCC4 domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0004518   nuclease activity  
GO:0003677   DNA binding  

Metabolic Pathways

Nucleotide excision repair (KEGG)

Structural information

Modbase 3D models:

There are 9 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
18 78 2mu3 (A) 102 165 46.00 0.068 0.02 0.251113 1.87
875 957 5d2s (A) 100 175 20.00 0 0.07 0.414129 -3.08
876 926 4o9b (A) 284 334 24.00 0 0.01 0.647542 -4.31
1192 1273 1yd6 (A) 13 95 15.00 0.61 0.15 0.226342 -0.54
1612 1858 2bgw (A) 12 228 21.00 0.0056 0.46 0.106712 1.07
1620 1697 1j23 (A) 6 83 37.00 0.00000012 0.59 0.470393 -0.17
1879 1960 2ebu (A) 403 485 11.00 0.48 0 0.210342 -0.93
1977 2049 4bxo (B) 135 214 16.00 0.000098 0.74 0.359958 -1.13
1979 2052 2aq0 (A) 1 75 32.00 0.00000077 1 0.523445 -1

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 VEG Tachyzoite, ME49 Tachyzoite, ME49 Oocyst, ME49 Bradyzoite. Gregory Fritz HM Sibley/Greg
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile ME49 merozoite. Hehl AB
Show/Hide expression data references
  • Fritz HM Transcriptomic analysis of toxoplasma development reveals many novel functions and structures specific to sporozoites and oocysts.
  • Gregory ToxoDB
  • Sibley/Greg ToxoDB
  • 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_127977)

Species Accession Gene Product
Arabidopsis thaliana AT5G41150   DNA repair endonuclease UVH1
Babesia bovis BBOV_IV002550   DNA repair endonuclease, putative
Brugia malayi Bm1_46945   ERCC4 domain containing protein
Candida albicans CaO19.12779   UV endonuclease
Candida albicans CaO19.5319   UV endonuclease
Candida albicans CaO19.5318   UV endonuclease
Candida albicans CaO19.12778   UV endonuclease
Caenorhabditis elegans CELE_C47D12.8   Protein C47D12.8
Cryptosporidium hominis Chro.40338   UV endonuclease; Rad1p
Cryptosporidium parvum cgd4_2960   ERCC4/XP-G-type excision repair nuclease
Cryptosporidium parvum cgd4_2970   RAD1, NH2 terminal ERCC4-like helicase domain
Dictyostelium discoideum DDB_G0284419   DNA excision repair protein 4
Drosophila melanogaster Dmel_CG3697   meiotic 9
Echinococcus granulosus EgrG_000580700   dna repair endonuclease xpf
Entamoeba histolytica EHI_148310   DNA repair endonuclease, putative
Echinococcus multilocularis EmuJ_000580700   dna repair endonuclease xpf
Homo sapiens ENSG00000175595   excision repair cross-complementation group 4
Loa Loa (eye worm) LOAG_00528   ERCC4 domain-containing protein
Mus musculus 50505   excision repair cross-complementing rodent repair deficiency, complementation group 4
Neospora caninum NCLIV_043890   Protein C47D12.8, partially confirmed by transcript evidence, related
Oryza sativa 4331279   Os03g0100400
Plasmodium berghei PBANKA_1144700   DNA repair endonuclease, putative
Plasmodium falciparum PF3D7_1368800   DNA repair endonuclease, putative
Plasmodium knowlesi PKNH_1102400   DNA repair endonuclease, putative
Plasmodium vivax PVX_115400   DNA repair endonuclease, putative
Plasmodium yoelii PY04288   DNA repair endonuclease, subunit
Saccharomyces cerevisiae YPL022W   Rad1p
Schistosoma japonicum Sjp_0081630   ko:K01175 excision repair cross-complementing rodent repair deficiency, complementation group 4 [EC:3.1.-.-], putative
Schistosoma japonicum Sjp_0099170   ko:K01175 excision repair cross-complementing rodent repair deficiency, complementation group 4 [EC:3.1.-.-], putative
Schistosoma mansoni Smp_153770   DNA repair endonuclease xp-f / mei-9 / rad1
Schmidtea mediterranea mk4.000684.11   DNA repair endonuclease XPF
Schmidtea mediterranea mk4.000684.10  
Schmidtea mediterranea mk4.000684.07   DNA repair endonuclease XPF
Toxoplasma gondii TGME49_305310   ERCC4 domain-containing protein
Theileria parva TP03_0395   DNA repair endonuclease, putative
Trichomonas vaginalis TVAG_447530   nuclease Rad1

Essentiality

TGME49_305310 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
CELE_C47D12.8 Caenorhabditis elegans embryonic lethal wormbase
CELE_C47D12.8 Caenorhabditis elegans slow growth wormbase
PBANKA_1144700 Plasmodium berghei Slow plasmo
TGME49_305310 this record Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.

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
Species Known druggable target Linked compounds Reference
Homo sapiens excision repair cross-complementation group 4 Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0046 0.4902 0
0.0046 0.4902 0
0.0046 0.4902 0
0.0046 0.4902 0
0.0115 0.6659 0.6659
0.0046 0.4902 0
0.0046 0.4902 0
0.0046 0.4902 0
0.034 0.5146 0.6834
0.0046 0.4902 0
0.0046 0.6659 0.6659
0.0038 0.6567 0.6567
0.0046 0.6659 0.6659
0.00518912 0.499306 0
0.0297 0.6834 0.6834
0.0046 0.6659 0.6659
0.0082 0.4902 0
0.0184 0.4148 0.6659
0.00558053 0.67155 0.67155
0.0046 0.4902 0
0.0046 0.4902 0
0.0046 0.4902 0
0.0039 0.6659 0.6659
0.0046 0.4902 0
0.0046 0.4902 0
0.0277 0.6793 0.6793
0.0046 0.4902 0
0.0046 0.4902 0
0.0046 0.6659 0.6659
0.0046 0.4902 0
0.0046 0.4902 0
0.0037 0.6659 0.6659
0.0299 0.6659 0.6659
0.0369 0.257 0.6906
0.0046 0.6659 0.6659
0.0244 0.5306 0.7075
0.0038 0.4902 0
0.0154 0.6758 0.6659
0.0043 0.4902 0
0.0046 0.4902 0
0.0046 0.4902 0
0.0046 0.6659 0.6659
0.0046 0.4902 0
0.0041 0.6659 0.6659
0.0296 0.6659 0.6659
0.0046 0.6659 0.6659
0.0046 0.6659 0.6659
0.0046 0.4902 0
0.0046 0.4902 0
0.0046 0.6659 0.6659
0.0046 0.4902 0
0.0041 0.4902 0
0.0046 0.4902 0
0.034 0.5146 0.6834
0.0046 0.6659 0.6659
0.0046 0.6659 0.6659
0.0046 0.4902 0
0.0115 0.4902 0
0.016 0.3018 0.5762
0.00567425 0.642712 0.642712
0.0046 0.4902 0
0.0046 0.4902 0
0.0046 0.4902 0
0.0037 0.4902 0
0.0046 0.6659 0.6659
0.0046 0.4902 0
0.00549578 0.603304 0.601256
0.0046 0.4902 0
0.0046 0.4902 0
0.0046 0.6659 0.6659
0.0038 0.4902 0
0.0293 0.6793 0.6793
0.0046 0.6659 0.6659
0.0046 0.4902 0
0.0037 0.6659 0.6659
0.004 0.4902 0.2531
0.0046 0.6659 0.6659
0.0039 0.4902 0
0.0046 0.6659 0.6659
0.0046 0.4902 0
0.0369 0.257 0.6906
0.0046 0.4902 0
0.0046 0.4902 0
0.0046 0.4902 0
0.0037 0.4902 0
0.0046 0.4902 0
0.0046 0.4902 0
0.0046 0.4902 0
0.0038 0.676 0.6659
0.0046 0.5491 0.4409
0.0041 0.4902 0
0.0043 0.4902 0
0.0173 0.2766 0

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_305310 (Toxoplasma gondii), ERCC4 domain-containing protein
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