Detailed view for PF3D7_1019800

Basic information

TDR Targets ID: 1267
Plasmodium falciparum, tRNA methyltransferase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 10.221 | Length (AA): 1084 | MW (Da): 130518 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 3

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

PF03054   tRNA methyl transferase

Gene Ontology

Mouse over links to read term descriptions.
No GO information for this protein.

Metabolic Pathways

Sulfur relay system (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
393 1044 1j7n (A) 32 721 17.00 0.0000058 0.72 0.49 1.16
210 400 4uos (A) 2 181 21.00 0.22 0.32 0.321599 -0.45
446 754 2der (B) 4 236 28.00 0 1 0.0904554 1.13
449 729 2hma (A) 8 214 33.00 0.00000000018 1 0.118825 1.61
142 327 4uos (A) 2 184 20.00 0.29 0.19 0.432063 -1.34
392 1062 5czz (A) 230 832 25.00 0.94 0.58 0.429385 2.51
472 983 2der (B) 12 360 21.00 0 0.83 -0.0347201 2.54
560 704 4dph (B) 168 373 31.00 0.88 0.03 0.11302 2.02

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 intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, early trophozoite, late trophozoite, Sporozoite, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 16 hs, Oocyst, Ring, Female Gametocyte. Otto TD Zanghi G Lasonder E
Show/Hide expression data references
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB

Orthologs

Ortholog group members (OG5_127383)

Species Accession Gene Product
Arabidopsis thaliana AT1G51310   tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase
Babesia bovis BBOV_III005960   tRNA methyl transferase family protein
Brugia malayi Bm1_08740   tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase
Candida albicans CaO19.7245   similar to S. cerevisiae YDL033C
Caenorhabditis elegans CELE_B0035.16   Protein B0035.16
Chlamydia trachomatis CT_287   tRNA-specific 2-thiouridylase MnmA
Dictyostelium discoideum DDB_G0288979   tRNA -methyltransferase
Drosophila melanogaster Dmel_CG3021   CG3021 gene product from transcript CG3021-RA
Escherichia coli b1133   tRNA(Gln,Lys,Glu) U34 2-thiouridylase, first step in mnm(5)-s(2)U34-tRNA synthesis
Echinococcus granulosus EgrG_001192300   mitochondrial tRNA specific 2 thiouridylase
Echinococcus multilocularis EmuJ_001192300   mitochondrial tRNA specific 2 thiouridylase
Homo sapiens ENSG00000100416   tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase
Leishmania braziliensis LbrM.07.0130   tRNA-methyl transferase, putative
Leishmania donovani LdBPK_070280.1   tRNA-methyl transferase, putative
Leishmania infantum LinJ.07.0280   tRNA-methyl transferase, putative
Leishmania major LmjF.07.0130   tRNA-methyl transferase, putative
Leishmania mexicana LmxM.07.0130   tRNA-methyl transferase, putative
Loa Loa (eye worm) LOAG_02754   hypothetical protein
Mycobacterium leprae ML1707c   probable tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase TrmU
Mus musculus ENSMUSG00000022386   tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase
Mycobacterium tuberculosis Rv3024c   Probable tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase TrmU
Mycobacterium ulcerans MUL_1928   tRNA-specific 2-thiouridylase MnmA
Neospora caninum NCLIV_053570   tRNA methyltransferase domain-containing protein, putative
Oryza sativa 4331793   Os03g0174600
Plasmodium berghei PBANKA_0504000   tRNA methyltransferase, putative
Plasmodium falciparum PF3D7_1019800   tRNA methyltransferase, putative
Plasmodium knowlesi PKNH_0604000   tRNA methyltransferase, putative
Plasmodium vivax PVX_001855   tRNA methyltransferase, putative
Plasmodium yoelii PY00607   probable tRNA-methyltransferase
Saccharomyces cerevisiae YDL033C   Slm3p
Schistosoma japonicum Sjp_0015200   ko:K00566 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [EC2.1.1.61], putative
Schistosoma mansoni Smp_113390   tRNA(5-methylaminomethyl-2-thiouridylate)-methy lt ransferase
Schistosoma mansoni Smp_178920   tRNA(5-methylaminomethyl-2-thiouridylate)-methy lt ransferase
Schmidtea mediterranea mk4.015951.00   Probable mitochondrial tRNA-specific 2-thiouridylase 1
Schmidtea mediterranea mk4.066048.00  
Schmidtea mediterranea mk4.034030.00   Probable mitochondrial tRNA-specific 2-thiouridylase 1
Schmidtea mediterranea mk4.040827.00  
Trypanosoma brucei gambiense Tbg972.8.1460   tRNA-methyl transferase, putative
Trypanosoma brucei Tb927.8.1830   tRNA-methyl transferase, putative
Trypanosoma congolense TcIL3000_8_1760   tRNA-methyl transferase, putative
Toxoplasma gondii TGME49_309110   tRNA methyl transferase
Theileria parva TP02_0339   tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0155   tRNA-specific 2-thiouridylase MnmA

Essentiality

PF3D7_1019800 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.1830 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.8.1830 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.8.1830 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.8.1830 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
b1133 Escherichia coli essential goodall
PBANKA_0504000 Plasmodium berghei Essential plasmo
TGME49_309110 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
  • 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.
  • 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
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • 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

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): 0.1

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

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Gene identifier PF3D7_1019800 (Plasmodium falciparum), tRNA methyltransferase, putative
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