Detailed view for TGME49_202770

Basic information

TDR Targets ID: 257565
Toxoplasma gondii, RNA recognition motif-containing protein
Source Database / ID:  ToxoDB 

pI: 6.1842 | Length (AA): 532 | MW (Da): 55868 | 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

PF00076   RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

Gene Ontology

Mouse over links to read term descriptions.
GO:0003676   nucleic acid binding  
GO:0000166   nucleotide binding  

Metabolic Pathways

Spliceosome (KEGG)

Structural information

Modbase 3D models:

There are 8 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
76 148 2g4b (A) 260 334 25.00 0.000094 1 0.66 -2.11
207 333 1u6f (A) 1 126 26.00 0.000000036 1 0.57 0.09
444 530 1opi (A) 377 474 36.00 0.000000036 1 0.61 -1.18
74 326 2qfj (A) 111 285 44.00 0 1 0.448964 0.89
76 150 2mb0 (B) 9 85 36.00 0.000071 1 0.745377 -1.72
436 532 3dxb (A) 452 556 46.00 0 1 0.825731 -1.71
468 532 2mkc (A) 31 101 25.00 0.55 0.75 0.25598 0.67
476 528 2d9p (A) 324 376 19.00 0.33 0.07 0.114424 1.48

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, ME49 merozoite, ME49 Oocyst, ME49 Bradyzoite. Gregory Hehl AB Fritz HM Sibley/Greg
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_130752)

Species Accession Gene Product
Brugia malayi Bm1_55125   Rnp
Caenorhabditis elegans CELE_Y47G6A.20   Protein RNP-6, isoform C
Cryptosporidium hominis Chro.10308   RNA-binding protein SiahBP
Cryptosporidium parvum cgd1_2730   Ro ribonucleoprotein-binding protein 1, RNA binding protein with 3x RRM domains
Dictyostelium discoideum DDB_G0285403   RNA recognition motif-containing protein RRM
Drosophila melanogaster Dmel_CG12085   poly U binding factor 68kD
Echinococcus granulosus EgrG_000800800   Poly U binding splicing factor half pint
Echinococcus granulosus EgrG_001087600   polyU binding splicing factor PUF60
Echinococcus multilocularis EmuJ_000800800   Poly U binding splicing factor half pint
Echinococcus multilocularis EmuJ_001087600   poly(U) binding splicing factor PUF60
Homo sapiens ENSG00000179950   poly-U binding splicing factor 60KDa
Loa Loa (eye worm) LOAG_09546   Poly(U)-binding-splicing factor half pint
Mus musculus ENSMUSG00000002524   poly-U binding splicing factor 60
Neospora caninum NCLIV_022140   GA11385, related
Schistosoma japonicum Sjp_0074440   Poly(U)-binding-splicing factor PUF60-B, putative
Schistosoma japonicum Sjp_0020100   Poly(U)-binding-splicing factor PUF60-B, putative
Schistosoma mansoni Smp_129720   fuse-binding protein-interacting repressor siahbp1
Schistosoma mansoni Smp_012900   fuse-binding protein-interacting repressor siahbp1
Schmidtea mediterranea mk4.002220.07   Poly(U)-binding-splicing factor PUF60
Schmidtea mediterranea mk4.002440.03   Poly(U)-binding-splicing factor PUF60
Toxoplasma gondii TGME49_202770   RNA recognition motif-containing protein
Theileria parva TP04_0540   hypothetical protein

Essentiality

TGME49_202770 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
CELE_Y47G6A.20 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y47G6A.20 Caenorhabditis elegans larval lethal wormbase
CELE_Y47G6A.20 Caenorhabditis elegans slow growth wormbase
CELE_Y47G6A.20 Caenorhabditis elegans sterile wormbase
TGME49_202770 this record Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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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User comments

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Gene identifier TGME49_202770 (Toxoplasma gondii), RNA recognition motif-containing protein
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