Detailed view for PF3D7_1459700

Basic information

TDR Targets ID: 2900
Plasmodium falciparum, pyridoxal 5'-phosphate synthase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.8139 | Length (AA): 287 | MW (Da): 32960 | 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

PF03853   YjeF-related protein N-terminus

Gene Ontology

Mouse over links to read term descriptions.
GO:0003674   molecular_function  
GO:0008150   biological_process  
GO:0005575   cellular_component  

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
1 182 1jzt (A) 20 223 44.00 0 1 1.54 -1.54
4 166 2ax3 (A) 11 178 33.00 0 1 1.43 -1.57
33 287 3d3k (A) 258 505 20.00 0 1 1.1251 -0.64
60 287 2o8n (A) 26 257 42.00 0 1 1.36253 -1.08

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 gametocyte, early schizont, late trophozoite. PlasmoDB
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 32 hs, sporozoite, early trophozoite, late schizont, Oocyst, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 16 hs, intra-erythrocytic - 48 hs, Ring, Sporozoite. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 40 hs, Male Gametocyte. Otto TD Lasonder E
Show/Hide expression data references
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

Orthologs

Ortholog group members (OG5_128872)

Species Accession Gene Product
Arabidopsis thaliana AT5G49970   pyridoxine/pyridoxamine 5'-phosphate oxidase 1
Brugia malayi Bm1_49840   YjeF-related protein N-terminus containing protein
Candida albicans CaO19.3679   similar to S. cerevisiae YNL200C
Candida albicans CaO19.11163   similar to S. cerevisiae YNL200C
Caenorhabditis elegans CELE_Y18D10A.3   Protein Y18D10A.3
Dictyostelium discoideum DDB_G0269890   hypothetical protein
Drosophila melanogaster Dmel_CG2974   CG2974 gene product from transcript CG2974-RB
Echinococcus granulosus EgrG_000736050   apolipoprotein A I binding protein
Entamoeba histolytica EHI_136490   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_000736050   apolipoprotein A I binding protein
Giardia lamblia GL50803_17366   Pyridoxamine 5-phosphate oxidase, putative
Homo sapiens ENSG00000163382   apolipoprotein A-I binding protein
Loa Loa (eye worm) LOAG_03083   hypothetical protein
Mus musculus ENSMUSG00000028070   apolipoprotein A-I binding protein
Neospora caninum NCLIV_065800   hypothetical protein
Oryza sativa 4348496   Os10g0377800
Plasmodium berghei PBANKA_1323300   pyridoxal 5'-phosphate synthase, putative
Plasmodium falciparum PF3D7_1459700   pyridoxal 5'-phosphate synthase, putative
Plasmodium knowlesi PKNH_1222100   pyridoxal 5'-phosphate synthase, putative
Plasmodium vivax PVX_117475   hypothetical protein, conserved
Plasmodium yoelii PY05519   Homo sapiens TGR-CL10C
Saccharomyces cerevisiae YNL200C   NADHX epimerase
Schistosoma japonicum Sjp_0006580   Apolipoprotein A-I-binding protein precursor, putative
Schistosoma mansoni Smp_142640   n-terminal yjef related
Schmidtea mediterranea mk4.005551.03   NAD(P)H-hydrate epimerase
Schmidtea mediterranea mk4.002833.02  
Toxoplasma gondii TGME49_249650   apolipoprotein A-I binding protein, putative

Essentiality

PF3D7_1459700 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_1323300 Plasmodium berghei Dispensable plasmo
TGME49_249650 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource

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

3 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

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier PF3D7_1459700 (Plasmodium falciparum), pyridoxal 5'-phosphate synthase, putative
Title for this comment
Comment