Detailed view for TGME49_310060

Basic information

TDR Targets ID: 261987
Toxoplasma gondii, small nuclease
Source Database / ID:  ToxoDB 

pI: 7.3554 | Length (AA): 367 | MW (Da): 41322 | 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

PF00929   Exonuclease

Gene Ontology

Mouse over links to read term descriptions.
GO:0005622   intracellular  
GO:0004527   exonuclease activity  
GO:0003676   nucleic acid binding  
GO:0000175   3'-5'-exoribonuclease activity  

Metabolic Pathways

Ribosome biogenesis in eukaryotes (KEGG)

Structural information

Modbase 3D models:

There are 2 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
184 366 1j9a (A) 3 185 49.00 0 1 1.13004 -0.62
187 366 5cy4 (A) 4 183 48.00 0 1 1.12756 -0.81

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
Upper 80-100% percentile VEG Tachyzoite, ME49 Tachyzoite. Gregory
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile ME49 merozoite, ME49 Bradyzoite. Hehl AB Sibley/Greg
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile ME49 Oocyst. Fritz HM
Show/Hide expression data references
  • 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.
  • Sibley/Greg ToxoDB

Orthologs

Ortholog group members (OG5_129087)

Species Accession Gene Product
Arabidopsis thaliana AT2G26970   polynucleotidyl transferase, ribonuclease H-like superfamily protein
Brugia malayi Bm1_35405   Smfn protein
Candida albicans CaO19.1466   RNA endonuclease
Candida albicans CaO19.9041   RNA endonuclease
Caenorhabditis elegans CELE_C08B6.8   Protein C08B6.8, isoform B
Dictyostelium discoideum DDB_G0273741   RNA exonuclease 2
Dictyostelium discoideum DDB_G0273355   RNA exonuclease 2
Drosophila melanogaster Dmel_CG10214   CG10214 gene product from transcript CG10214-RA
Escherichia coli b4162   oligoribonuclease
Homo sapiens ENSG00000076043   RNA exonuclease 2
Loa Loa (eye worm) LOAG_01772   smfn protein
Mycobacterium leprae ML0427c   Probable oligoribonuclease Orn
Mus musculus ENSMUSG00000032026   REX2, RNA exonuclease 2 homolog (S. cerevisiae)
Mycobacterium tuberculosis Rv2511   Oligoribonuclease Orn
Mycobacterium ulcerans MUL_3790   oligoribonuclease
Neospora caninum NCLIV_054180   Oligoribonuclease, related
Oryza sativa 9270337   Os04g0303950
Oryza sativa 4329319   Os02g0465500
Onchocerca volvulus OVOC11448   Putative oligoribonuclease
Saccharomyces cerevisiae YLR059C   Rex2p
Toxoplasma gondii TGME49_310060   small nuclease

Essentiality

TGME49_310060 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
b4162 Escherichia coli essential goodall
YLR059C Saccharomyces cerevisiae inviable yeastgenome
TGME49_310060 this record Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource

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

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier TGME49_310060 (Toxoplasma gondii), small nuclease
Title for this comment
Comment