Detailed view for PF3D7_1349100

Basic information

TDR Targets ID: 162
Plasmodium falciparum, nucleoside diphosphate hydrolase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 5.8064 | Length (AA): 196 | MW (Da): 23263 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG2

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

PF00293   NUDIX domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0006139   nucleobase, nucleoside, nucleotide and nucleic acid metabolic process  
GO:0016787   hydrolase activity  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 7 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
13 181 2fkb (A) 8 167 25.00 0 1 1.21 -0.98
1 196 3dup (A) 69 279 15.00 0 1 1.1238 -0.06
13 181 2fkb (A) 8 167 26.00 0 1 1.23344 -0.73
145 192 3htk (A) 315 363 44.00 0.31 0.03 0.597798 0.23
3 192 2pny (A) 2 220 21.00 0 1 1.07859 -0.43
5 112 3fcm (A) 1 104 38.00 0.36 0.71 0.68012 1.15
13 181 2fkb (A) 8 167 26.00 0 1 1.22334 -0.66

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 Oocyst. Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, early schizont, Sporozoite, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 32 hs, early trophozoite, late trophozoite. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, Ring. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Female Gametocyte. 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.
  • 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.

Orthologs

Ortholog group members (OG5_131701)

Species Accession Gene Product
Arabidopsis thaliana AT1G79690   nudix hydrolase 3
Babesia bovis BBOV_III000620   hydrolase, NUDIX family protein
Babesia bovis BBOV_III000640   hydrolase, NUDIX family protein
Dictyostelium discoideum DDB_G0269784   hypothetical protein
Dictyostelium discoideum DDB_G0275419   hypothetical protein
Escherichia coli b2299   putative NUDIX hydrolase
Giardia lamblia GL50803_16623   Hypothetical protein
Oryza sativa 4330987   Os02g0793300
Plasmodium berghei PBANKA_1361900   nucleoside diphosphate hydrolase, putative
Plasmodium falciparum PF3D7_1349100   nucleoside diphosphate hydrolase, putative
Plasmodium knowlesi PKNH_1251800   nucleoside diphosphate hydrolase, putative
Plasmodium vivax PVX_083350   nucleoside diphosphate hydrolase, putative
Plasmodium yoelii PY02890   hypothetical protein
Theileria parva TP03_0766   nucleoside diphospahte hydrolase, putative

Essentiality

PF3D7_1349100 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b2299 Escherichia coli non-essential goodall
PBANKA_1361900 Plasmodium berghei Dispensable plasmo
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.
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

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

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Gene identifier PF3D7_1349100 (Plasmodium falciparum), nucleoside diphosphate hydrolase, putative
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