Detailed view for TGME49_272270

Basic information

TDR Targets ID: 258634
Toxoplasma gondii, radical SAM domain-containing protein
Source Database / ID:  ToxoDB 

pI: 7.2905 | Length (AA): 1166 | MW (Da): 126166 | Paralog Number: 1

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

PF04055   Radical SAM superfamily
PF08608   Wyosine base formation

Gene Ontology

Mouse over links to read term descriptions.
GO:0051539   4 iron, 4 sulfur cluster binding  
GO:0051536   iron-sulfur cluster binding  
GO:0003824   catalytic activity  
GO:0008033   tRNA processing  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 4 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
272 603 1ja1 (A) 63 360 16.00 0 0.93 0.07 1.04
287 482 2bmv (A) 2 164 12.00 0 0.27 0.15 -0.35
668 961 2yx0 (A) 17 317 32.00 0.000000046 1 0.645044 -0.29
670 899 2z2u (A) 1 231 38.00 0 1 0.575856 -0.19

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. Gregory Hehl AB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile VEG Tachyzoite, ME49 Oocyst, ME49 Bradyzoite. Gregory Fritz HM Sibley/Greg
Show/Hide expression data references
  • Sibley/Greg ToxoDB
  • Fritz HM Transcriptomic analysis of toxoplasma development reveals many novel functions and structures specific to sporozoites and oocysts.
  • Gregory 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_128065)

Species Accession Gene Product
Arabidopsis thaliana AT1G75200   tRNA wybutosine-synthesizing protein 1-like protein
Babesia bovis BBOV_IV001010   conserved hypothetical protein
Candida albicans CaO19.10974   similar to S. cerevisiae YPL207W
Candida albicans CaO19.3470   similar to S. cerevisiae YPL207W
Homo sapiens ENSG00000277149   tRNA-yW synthesizing protein 1 homolog B (S. cerevisiae)
Homo sapiens ENSG00000198874   tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)
Leishmania braziliensis LbrM.15.1540   hypothetical protein, conserved
Leishmania braziliensis LbrM.05.0730   hypothetical protein, conserved
Leishmania donovani LdBPK_151610.1   Radical SAM superfamily/Wyosine base formation, putative
Leishmania donovani LdBPK_050750.1   Flavodoxin/Radical SAM superfamily/Wyosine base formation, putative
Leishmania infantum LinJ.15.1610   hypothetical protein, conserved
Leishmania infantum LinJ.05.0750   hypothetical protein, conserved
Leishmania major LmjF.15.1540   hypothetical protein, conserved
Leishmania major LmjF.05.0750   hypothetical protein, conserved
Leishmania mexicana LmxM.05.0750   hypothetical protein, conserved
Leishmania mexicana LmxM.15.1540   hypothetical protein, conserved
Mus musculus ENSMUSG00000056310   tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)
Neospora caninum NCLIV_035010   hypothetical protein
Neospora caninum NCLIV_058590   hypothetical protein
Oryza sativa 4334285   Os03g0775300
Plasmodium berghei PBANKA_1239700   S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase, putative
Plasmodium falciparum PF3D7_0524900   S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase, putative
Plasmodium knowlesi PKNH_1007900   S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase, putative
Plasmodium vivax PVX_080000   hypothetical protein, conserved
Plasmodium yoelii PY05984   moaA / nifB / pqqE family, putative
Saccharomyces cerevisiae YPL207W   Tyw1p
Schmidtea mediterranea mk4.005494.00  
Trypanosoma brucei gambiense Tbg972.9.2650   radical SAM domain protein, putative
Trypanosoma brucei gambiense Tbg972.7.8390   hypothetical protein, conserved
Trypanosoma brucei Tb927.9.4950   radical SAM domain protein, putative
Trypanosoma brucei Tb927.7.7130   S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase, putative
Trypanosoma congolense TcIL3000_9_1630   radical SAM domain protein, putative
Trypanosoma congolense TcIL3000_7_5820   Radical SAM superfamily/Wyosine base formation, putative
Trypanosoma cruzi TcCLB.504175.9   Flavodoxin/Radical SAM superfamily/Wyosine base formation, putative
Trypanosoma cruzi TcCLB.478671.9   Flavodoxin/Radical SAM superfamily/Wyosine base formation, putative
Trypanosoma cruzi TcCLB.508277.60   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.510613.10   Flavodoxin/Radical SAM superfamily/Wyosine base formation, putative
Toxoplasma gondii TGME49_272270   radical SAM domain-containing protein
Toxoplasma gondii TGME49_315962   hypothetical protein
Theileria parva TP01_0125   hypothetical protein, conserved

Essentiality

TGME49_272270 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb09.160.3520 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.160.3520 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb09.160.3520 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb09.160.3520 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Tb927.7.7130 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.7.7130 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.7.7130 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.7.7130 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
YPL207W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1239700 Plasmodium berghei Essential plasmo
TGME49_272270 this record Toxoplasma gondii Probably non-essential sidik
TGME49_315962 Toxoplasma gondii Probably non-essential sidik
TGME49_272270 this record Toxoplasma gondii Essentiality uncertain sidik
TGME49_315962 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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.
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection

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_272270 (Toxoplasma gondii), radical SAM domain-containing protein
Title for this comment
Comment