Detailed view for TGME49_216390

Basic information

TDR Targets ID: 262061
Toxoplasma gondii, RNA methyltransferase, TrmH family protein
Source Database / ID:  ToxoDB 

pI: 8.0763 | Length (AA): 840 | MW (Da): 89524 | 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

PF00588   SpoU rRNA Methylase family

Gene Ontology

Mouse over links to read term descriptions.
GO:0008173   RNA methyltransferase activity  
GO:0003723   RNA binding  
GO:0006396   RNA processing  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 11 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
531 803 1ipa (A) 1 261 19.00 0 1 0.39 -0.06
652 806 2ha8 (A) 23 178 17.00 0 0.97 0.38 -0.88
9 86 2khm (A) 10 90 32.00 0.96 0.01 0.192057 1.14
16 309 4k6j (A) 700 994 9.00 0 0.01 0.4099 -0.18
265 401 2y44 (A) 97 224 31.00 0.21 0.19 0.413195 -0.62
582 807 4x3l (A) 33 258 33.00 0 1 0.539148 0.29
614 801 2i6d (A) 56 252 26.00 0 1 0.50871 -0.01
642 801 1zjr (A) 12 170 26.00 0 1 0.526376 -0.49
644 817 1v2x (A) 11 182 18.00 0.00000018 0.97 0.413343 -0.27
652 798 5co4 (B) 0 141 33.00 0.014 0.88 0.4201 0.42
657 801 1gz0 (A) 97 240 22.00 0 1 0.467519 -0.38

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 merozoite, ME49 Oocyst, ME49 Bradyzoite. Gregory Hehl AB Fritz HM Sibley/Greg
Show/Hide expression data references
  • 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.
  • Gregory ToxoDB
  • Sibley/Greg ToxoDB

Orthologs

Ortholog group members (OG5_130184)

Species Accession Gene Product
Arabidopsis thaliana AT4G38020   tRNA/rRNA methyltransferase (SpoU) family protein
Chlamydia trachomatis CT_403   SpoU family rRNA methylase
Drosophila melanogaster Dmel_CG14100   CG14100 gene product from transcript CG14100-RA
Homo sapiens ENSG00000171861   RNA methyltransferase like 1
Mycobacterium leprae ML1397   Possible 23S rRNA methyltransferase TsnR
Mus musculus ENSMUSG00000038046   RNA methyltransferase like 1
Mycobacterium tuberculosis Rv1644   Possible 23S rRNA methyltransferase TsnR
Mycobacterium ulcerans MUL_1630   23S rRNA methyltransferase TsnR
Neospora caninum NCLIV_059850   RRNA methylase, related
Oryza sativa 4333747   Os03g0685100
Schistosoma japonicum Sjp_0302510   RNA methyltransferase-like protein 1B, putative
Schistosoma mansoni Smp_123530   rna methyltransferase-related
Toxoplasma gondii TGME49_216390   RNA methyltransferase, TrmH family protein

Essentiality

TGME49_216390 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
TGME49_216390 this record Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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.
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.

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

2 literature references were collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

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Gene identifier TGME49_216390 (Toxoplasma gondii), RNA methyltransferase, TrmH family protein
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