Detailed view for TGME49_224860

Basic information

TDR Targets ID: 258859
Toxoplasma gondii, exosome component 2, putative
Source Database / ID:  ToxoDB 

pI: 8.793 | Length (AA): 353 | MW (Da): 38735 | Paralog Number: 0

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

Druggability Group : DG1

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

PF14382   Exosome complex exonuclease RRP4 N-terminal region
PF15985   KH domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0000178   exosome (RNase complex)  
GO:0003723   RNA binding  
GO:0003676   nucleic acid binding  

Metabolic Pathways

RNA degradation (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
11 55 4xa1 (D) 13 1209 18.00 0 0.02 0.303279 -0.12
12 77 2l9l (A) 4 66 30.00 0 0.03 0.293769 1.3
57 347 4oo1 (H) 6 351 34.00 0 1 1.06816 0.68
82 352 2nn6 (H) 25 292 39.00 0 1 1.09601 0.74
84 159 3m7n (A) 4 79 43.00 0.0000000082 0.82 0.488997 1.51
137 214 1sro (A) 5 74 24.00 0 0.91 0.299763 0.94

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 60-80% percentile ME49 Tachyzoite, ME49 merozoite, ME49 Oocyst. Gregory Hehl AB Fritz HM
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile VEG Tachyzoite, ME49 Bradyzoite. Gregory 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.
  • Gregory ToxoDB
  • Fritz HM Transcriptomic analysis of toxoplasma development reveals many novel functions and structures specific to sporozoites and oocysts.
  • Sibley/Greg ToxoDB

Orthologs

Ortholog group members (OG5_127653)

Species Accession Gene Product
Arabidopsis thaliana AT1G03360   ribosomal RNA processing protein 4
Babesia bovis BBOV_III010600   conserved hypothetical protein
Brugia malayi Bm1_33895   exosome component 2
Candida albicans CaO19.8884   similar to S. cerevisiae RRP4 (YHR069C) exosome component involved mRNA degradation and nuclear RNA processing
Candida albicans CaO19.1304   similar to S. cerevisiae RRP4 (YHR069C) exosome component involved mRNA degradation and nuclear RNA processing
Caenorhabditis elegans CELE_Y73B6BL.3   Protein EXOS-2
Cryptosporidium hominis Chro.80348   hypothetical protein
Cryptosporidium parvum cgd8_2980   hypothetical protein
Dictyostelium discoideum DDB_G0291310   hypothetical protein
Drosophila melanogaster Dmel_CG3931   CG3931 gene product from transcript CG3931-RA
Echinococcus granulosus EgrG_000535000   Exosome complex exonuclease RRP4
Entamoeba histolytica EHI_163510   exosome complex exonuclease RRP4, putative
Echinococcus multilocularis EmuJ_000535000   Exosome complex exonuclease RRP4
Giardia lamblia GL50803_33022   Hypothetical protein
Homo sapiens ENSG00000130713   exosome component 2
Leishmania braziliensis LbrM.14.0010   exosome complex exonuclease, putative,ribosomal RNA processing protein 4, putative
Leishmania donovani LdBPK_140010.1   exosome complex exonuclease, putative
Leishmania infantum LinJ.14.0010   exosome complex exonuclease, putative,ribosomal RNA processing protein 4, putative
Leishmania major LmjF.14.0010   exosome complex exonuclease, putative,ribosomal RNA processing protein 4, putative
Leishmania mexicana LmxM.14.0010   exosome complex exonuclease, putative,ribosomal RNA processing protein 4, putative
Loa Loa (eye worm) LOAG_00357   Rrp4-PA
Mus musculus ENSMUSG00000039356   exosome component 2
Neospora caninum NCLIV_047850   exosome complex exonuclease, putative
Oryza sativa 4336421   Os04g0520000
Plasmodium berghei PBANKA_1007800   exosome complex component RRP4, putative
Plasmodium falciparum PF3D7_0410400   exosome complex component RRP4, putative
Plasmodium knowlesi PKNH_0308500   exosome complex component RRP4, putative
Plasmodium vivax PVX_000730   exosome complex component RRP4, putative
Plasmodium yoelii PY02309   hypothetical protein
Saccharomyces cerevisiae YHR069C   Rrp4p
Schistosoma japonicum Sjp_0218320   ko:K03679 RNA-binding protein Rrp4 and related proteins, putative
Schistosoma mansoni Smp_064260   rrp4
Schmidtea mediterranea mk4.003371.01   Exosome complex component RRP4
Trypanosoma brucei gambiense Tbg972.7.5280   ribosomal RNA processing protein 4,exosome complex exonuclease
Trypanosoma brucei Tb927.7.4670   ribosomal RNA processing protein 4
Trypanosoma congolense TcIL3000_0_13330   ribosomal RNA processing protein 4
Trypanosoma cruzi TcCLB.510167.29   exosome complex exonuclease, putative
Trypanosoma cruzi TcCLB.508859.109   ribosomal RNA processing protein 4, putative
Toxoplasma gondii TGME49_224860   exosome component 2, putative
Theileria parva TP02_0081   hypothetical protein, conserved
Trichomonas vaginalis TVAG_246740   rrp4, putative

Essentiality

TGME49_224860 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.7.4670 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.7.4670 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.7.4670 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.7.4670 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
YHR069C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1007800 Plasmodium berghei Essential plasmo
TGME49_224860 this record Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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.
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

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.

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Gene identifier TGME49_224860 (Toxoplasma gondii), exosome component 2, putative
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