Detailed view for TGME49_250750

Basic information

TDR Targets ID: 260733
Toxoplasma gondii, tRNA (uracil-5-)-methyltransferase
Source Database / ID:  ToxoDB 

pI: 6.8459 | Length (AA): 1116 | MW (Da): 121269 | 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

PF01170   Putative RNA methylase family UPF0020
PF05958   tRNA (Uracil-5-)-methyltransferase

Gene Ontology

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

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 9 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
563 966 1uwv (A) 75 432 21.00 0 1 0.43 0.44
695 1050 1uir (A) 9 310 12.00 0 0.75 -0.03 0.66
757 1093 1m6y (A) 5 285 10.00 0 0.96 -0.1 1.15
764 956 2esr (A) 28 185 13.00 0 0.83 -0.01 -0.38
108 140 3bog (C) 3 67 48.00 0.035 0.15 0.58557 -0.68
711 966 1uwv (A) 222 432 27.00 0 1 0.340091 0.28
729 963 2jjq (A) 226 404 37.00 0.000000000006 1 0.285573 0.38
750 876 2avd (A) 80 173 24.00 0 0.93 0.0674993 0.08
800 995 5cwo (A) 5 215 26.00 0.67 1 0.556627 -1.38

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
Upper 80-100% percentile ME49 Oocyst. Fritz HM
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile ME49 Tachyzoite, ME49 Bradyzoite. Gregory Sibley/Greg
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile VEG Tachyzoite, ME49 merozoite. Gregory Hehl AB
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.
  • Sibley/Greg ToxoDB
  • Fritz HM Transcriptomic analysis of toxoplasma development reveals many novel functions and structures specific to sporozoites and oocysts.
  • Gregory ToxoDB

Orthologs

Ortholog group members (OG5_126903)

Species Accession Gene Product
Arabidopsis thaliana AT2G28450   zinc finger CCCH domain-containing protein 24
Arabidopsis thaliana AT3G21300   RNA methyltransferase family protein
Brugia malayi Bm1_52450   hypothetical protein
Candida albicans CaO19.11843   one of two potential tRNA (Uracil-5-)-methyltransferase genes
Candida albicans CaO19.3327   one of two potential tRNA (Uracil-5-)-methyltransferase genes
Candida albicans CaO19.10837   one of two potential tRNA (Uracil-5-)-methyltransferase genes
Candida albicans CaO19.4365   one of two potential tRNA (Uracil-5-)-methyltransferase genes
Caenorhabditis elegans CELE_H24K24.4   Protein H24K24.4
Cryptosporidium hominis Chro.20288   hypothetical protein
Cryptosporidium parvum cgd2_2710   TrmA RNA methylase
Chlamydia trachomatis CT_742   rRNA methyltransferse
Dictyostelium discoideum DDB_G0293244   hypothetical protein
Drosophila melanogaster Dmel_CG3808   CG3808 gene product from transcript CG3808-RA
Escherichia coli b2785   23S rRNA m(5)U1939 methyltransferase, SAM-dependent
Escherichia coli b0859   23S rRNA m(5)U747 methyltransferase, SAM-dependent
Echinococcus granulosus EgrG_001011250   tRNA uracil 5 methyltransferase A
Entamoeba histolytica EHI_047740   RNA methyltransferase, putative
Echinococcus multilocularis EmuJ_001011250   tRNA (uracil 5) methyltransferase A
Homo sapiens ENSG00000188917   tRNA methyltransferase 2 homolog B (S. cerevisiae)
Homo sapiens ENSG00000099899   tRNA methyltransferase 2 homolog A (S. cerevisiae)
Leishmania braziliensis LbrM.20.5870   hypothetical protein, conserved
Leishmania donovani LdBPK_201680.1   tRNA (Uracil-5-)-methyltransferase, putative
Leishmania infantum LinJ.20.1680   hypothetical protein, conserved
Leishmania major LmjF.20.1710   hypothetical protein, conserved
Leishmania mexicana LmxM.20.1710   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_03093   hypothetical protein
Loa Loa (eye worm) LOAG_07527   hypothetical protein
Mus musculus ENSMUSG00000067369   TRM2 tRNA methyltransferase 2B
Mus musculus ENSMUSG00000022721   TRM2 tRNA methyltransferase 2A
Mycobacterium tuberculosis Rv2689c   Conserved alanine and valine and glycine rich protein
Mycobacterium ulcerans MUL_3327   SAM-dependent methyltransferase
Neospora caninum NCLIV_035280   Methyltransferase, related
Neospora caninum NCLIV_066290   hypothetical protein
Oryza sativa 9271204   Os04g0105000
Oryza sativa 4327311   Os01g0193600
Onchocerca volvulus OVOC6615  
Plasmodium berghei PBANKA_0914600   RNA (uracil-5-)methyltransferase, putative
Plasmodium falciparum PF3D7_1133800   RNA (uracil-5-)methyltransferase, putative
Plasmodium knowlesi PKNH_0931900   RNA (uracil-5-)methyltransferase, putative
Plasmodium vivax PVX_092300   hypothetical protein, conserved
Plasmodium yoelii PY05313   unnamed protein product
Saccharomyces cerevisiae YKR056W   Trm2p
Schistosoma mansoni Smp_123520   rna m5u methyltransferase
Schmidtea mediterranea mk4.071798.02  
Schmidtea mediterranea mk4.071798.01  
Schmidtea mediterranea mk4.010005.04   tRNA
Schmidtea mediterranea mk4.011294.05   tRNA
Schmidtea mediterranea mk4.035241.00   tRNA
Trypanosoma brucei gambiense Tbg972.1.1860   hypothetical protein, conserved
Trypanosoma brucei Tb927.1.3050   tRNA (Uracil-5-)-methyltransferase, putative
Trypanosoma congolense TcIL3000_1_1470   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.508405.110   tRNA (Uracil-5-)-methyltransferase, putative
Trypanosoma cruzi TcCLB.506363.130   tRNA (Uracil-5-)-methyltransferase, putative
Toxoplasma gondii TGME49_250750   tRNA (uracil-5-)-methyltransferase
Toxoplasma gondii TGME49_271860   tRNA (Uracil-5-)-methyltransferase
Trichomonas vaginalis TVAG_151750   RNA m5u methyltransferase, putative

Essentiality

TGME49_250750 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.1.3050 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.1.3050 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.1.3050 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.1.3050 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
b0859 Escherichia coli non-essential goodall
b2785 Escherichia coli non-essential goodall
PBANKA_0914600 Plasmodium berghei Essential plasmo
TGME49_250750 this record Toxoplasma gondii Essentiality uncertain sidik
TGME49_271860 Toxoplasma gondii Essentiality uncertain sidik
TGME49_250750 this record Toxoplasma gondii Probably non-essential sidik
TGME49_271860 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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.

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

Druggability index (range: 0 to 1): 0.3

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_250750 (Toxoplasma gondii), tRNA (uracil-5-)-methyltransferase
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