Detailed view for PBANKA_1242500

Basic information

TDR Targets ID: 828745
Plasmodium berghei, ATP-dependent RNA helicase DDX41, putative
Source Database / ID: 

pI: 8.3111 | Length (AA): 632 | MW (Da): 71848 | Paralog Number: 0

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

Druggability Group : DG

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

PF00270   DEAD/DEAH box helicase
PF00271   Helicase conserved C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005524   ATP binding  
GO:0003676   nucleic acid binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 6 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
1 138 4uos (A) 31 177 20.00 0.038 0.05 0.536254 -1.99
69 569 2eyq (A) 460 949 16.00 0 1 0.772722 0.89
159 400 5h1y (A) 157 398 62.00 0 1 1.29091 -1.95
184 620 2zj5 (A) 2 467 16.00 0 1 0.670456 0.5
408 568 2p6n (A) 406 566 75.00 0 1 1.26975 -1.82
413 627 1oyw (A) 215 441 22.00 0.17 1 0.59009 -0.06

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 Ookinete, 4 hs Ring, 16 hs Trophozoite, Erthyrocytic stages, Female gametocyte, Male gametocyte. Otto TD Yeoh LM
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Gametocyte, 22 hs Schizont. Otto TD
Show/Hide expression data references
  • Otto TD A comprehensive evaluation of rodent malaria parasite genomes and gene expression.
  • Yeoh LM Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates.

Orthologs

Ortholog group members (OG5_129688)

Species Accession Gene Product
Arabidopsis thaliana AT5G51280   putative DEAD-box ATP-dependent RNA helicase 35
Arabidopsis thaliana AT4G33370   putative DEAD-box ATP-dependent RNA helicase 43
Brugia malayi Bm1_49040   DEAD
Caenorhabditis elegans CELE_H27M09.1   Protein SACY-1
Cryptosporidium hominis Chro.70507   RNA helicase-1
Cryptosporidium parvum cgd7_4600   abstrakt protein SF II helicase + Znknuckle C2HC (PA)
Dictyostelium discoideum DDB_G0287361   DEAD box protein abstrakt
Drosophila melanogaster Dmel_CG14637   abstrakt
Echinococcus granulosus EgrG_000941700   ATP dependent RNA helicase abstrakt
Echinococcus granulosus EgrG_000941800   ATP dependent RNA helicase abstrakt
Echinococcus multilocularis EmuJ_000941800   ATP dependent RNA helicase abstrakt
Echinococcus multilocularis EmuJ_000941700   ATP dependent RNA helicase abstrakt
Homo sapiens ENSG00000183258   DEAD (Asp-Glu-Ala-Asp) box polypeptide 41
Loa Loa (eye worm) LOAG_07898   ATP-dependent RNA helicase DDX41
Mus musculus ENSMUSG00000021494   DEAD (Asp-Glu-Ala-Asp) box polypeptide 41
Neospora caninum NCLIV_043620   hypothetical protein
Oryza sativa 4341945   Os06g0697200
Oryza sativa 4328308   Os02g0150100
Plasmodium berghei PBANKA_1242500   ATP-dependent RNA helicase DDX41, putative
Plasmodium falciparum PF3D7_0527900   ATP-dependent RNA helicase DDX41, putative
Plasmodium knowlesi PKNH_1004800   ATP-dependent RNA helicase DDX41, putative
Plasmodium vivax PVX_079855   RNA helicase-1, putative
Plasmodium yoelii PY01284   RNA helicase-1
Schistosoma japonicum Sjp_0118940   Probable ATP-dependent RNA helicase DDX41, putative
Schistosoma japonicum Sjp_0081620   ko:K01529 DEAD (Asp-Glu-Ala-Asp) box polypeptide 41 [EC:3.6.1.-], putative
Schistosoma japonicum Sjp_0132060   ko:K01529 abstrakt [EC:3.6.1.-], putative
Schistosoma mansoni Smp_172030   DEAD box ATP-dependent RNA helicase
Schmidtea mediterranea mk4.001812.02   Probable ATP-dependent RNA helicase DDX41
Schmidtea mediterranea mk4.000001.38   Probable ATP-dependent RNA helicase DDX41
Toxoplasma gondii TGME49_210360   DEAD (Asp-Glu-Ala-Asp) box polypeptide 41 family protein
Theileria parva TP02_0316   RNA helicase-1, putative

Essentiality

PBANKA_1242500 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
CELE_H27M09.1 Caenorhabditis elegans adult lethal wormbase
CELE_H27M09.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_H27M09.1 Caenorhabditis elegans larval arrest wormbase
CELE_H27M09.1 Caenorhabditis elegans slow growth wormbase
PBANKA_1242500 this record Plasmodium berghei Essential plasmo
TGME49_210360 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • 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
  • 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

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 PBANKA_1242500 (Plasmodium berghei), ATP-dependent RNA helicase DDX41, putative
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