Detailed view for PVX_122485

Basic information

TDR Targets ID: 266388
Plasmodium vivax, methionyl-tRNA formyltransferase, putative
Source Database / ID:  PlasmoDB 

pI: 10.2353 | Length (AA): 679 | MW (Da): 77693 | Paralog Number: 0

Signal peptide: Y | GPI Anchor: N | Predicted trans-membrane segments: 1

Druggability Group : DG5

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

PF00551   Formyl transferase
PF02911   Formyl transferase, C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0016742   hydroxymethyl-, formyl- and related transferase activity  
GO:0003824   catalytic activity  
GO:0009058   biosynthetic process  

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
262 670 2bw0 (A) 0 307 19.00 0 1 0.34 0.55
265 455 1meo (A) 2 189 16.00 0 0.99 0.57 -1.67
40 144 1r0r (E) 2 92 33.00 0.58 0.44 0.362539 -0.02
260 673 3r8x (A) 1 305 24.00 0 1 0.41892 1.23
260 464 3auf (A) 0 199 12.00 0 0.27 0.448115 -0.07
263 674 4iqf (A) 1 304 21.00 0 1 0.429975 1.09
264 423 4xcz (A) 1 143 28.00 0.23 0.98 0.410541 0.65
330 424 5cjj (A) 66 166 34.00 0.000073 0.31 0.267812 1.35
335 468 3tqr (A) 68 206 25.00 0.0035 0.9 0.455249 0.14

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 intraerythrocytic - 6 hs, intraerythrocytic - 12 hs, intraerythrocytic - 18 hs, intraerythrocytic - 24 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intraerythrocytic - 30 hs, intraerythrocytic - 36 hs, intraerythrocytic - 40 hs, intraerythrocytic - 48 hs. Zhu L
Show/Hide expression data references
  • Zhu L New insights into the Plasmodium vivax transcriptome using RNA-Seq.

Orthologs

Ortholog group members (OG5_127793)

Species Accession Gene Product
Arabidopsis thaliana AT1G66520   protein pigment defective 194
Candida albicans CaO19.4418   methionyl-tRNA transformylase
Candida albicans CaO19.11896   methionyl-tRNA transformylase
Chlamydia trachomatis CT_530   methionyl tRNAformyltransferase
Dictyostelium discoideum DDB_G0277347   hypothetical protein
Drosophila melanogaster Dmel_CG1750   CG1750 gene product from transcript CG1750-RA
Escherichia coli b3288   10-formyltetrahydrofolate:L-methionyl-tRNA(fMet) N-formyltransferase
Homo sapiens ENSG00000103707   mitochondrial methionyl-tRNA formyltransferase
Mycobacterium leprae ML0552   Probable methionyl-tRNA formyltransferase Fmt
Mus musculus ENSMUSG00000059183   mitochondrial methionyl-tRNA formyltransferase
Mycobacterium tuberculosis Rv1406   Probable methionyl-tRNA formyltransferase Fmt
Mycobacterium ulcerans MUL_1802   methionyl-tRNA formyltransferase
Neospora caninum NCLIV_050010   formyl transferase domain-containing protein, putative
Oryza sativa 4324118   Os01g0687500
Plasmodium berghei PBANKA_1411600   methionyl-tRNA formyltransferase, putative
Plasmodium falciparum PF3D7_1313200   methionyl-tRNA formyltransferase, putative
Plasmodium knowlesi PKNH_1413800   methionyl-tRNA formyltransferase, putative
Plasmodium vivax PVX_122485   methionyl-tRNA formyltransferase, putative
Plasmodium yoelii PY03768   methionyl-tRNA formyltransferase homolog, putative
Saccharomyces cerevisiae YBL013W   Fmt1p
Schistosoma japonicum Sjp_0041650   ko:K00604 methionyl-tRNA formyltransferase [EC2.1.2.9], putative
Schistosoma mansoni Smp_167310   methionyl-tRNA formyltransferase
Schmidtea mediterranea mk4.056090.01  
Schmidtea mediterranea mk4.000505.11   Methionyl-tRNA formyltransferase, mitochondrial
Schmidtea mediterranea mk4.040374.02  
Toxoplasma gondii TGME49_235640   formyl transferase domain-containing protein
Treponema pallidum TP0756   methionyl-tRNA formyltransferase (fmt)
Wolbachia endosymbiont of Brugia malayi Wbm0656   methionyl-tRNA formyltransferase

Essentiality

PVX_122485 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b3288 Escherichia coli essential goodall
TGME49_235640 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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.
  • 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
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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

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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Gene identifier PVX_122485 (Plasmodium vivax), methionyl-tRNA formyltransferase, putative
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