Detailed view for PF3D7_1425400

Basic information

TDR Targets ID: 2565
Plasmodium falciparum, DEAD/DEAH box helicase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 8.7985 | Length (AA): 1236 | MW (Da): 146282 | 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

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

Gene Ontology

Mouse over links to read term descriptions.
GO:0008150   biological_process  
GO:0005575   cellular_component  
GO:0008026   ATP-dependent helicase activity  
GO:0005524   ATP binding  
GO:0004386   helicase activity  
GO:0003887   DNA-directed DNA polymerase activity  
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 14 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
39 265 1vec (A) 83 281 13.00 0 0.17 0.22 -0.65
42 269 1t6n (A) 46 250 15.00 0 0.85 0.24 -0.71
654 811 2g2j (A) 307 473 11.00 0.00000000034 0.19 0.22 -0.85
11 885 3s5m (A) 196 1174 23.00 0.4 0.83 0.607029 1.6
37 310 4bgd (A) 456 729 25.00 0.00063 1 0.128783 0.69
39 274 5aga (A) 67 291 29.00 0 1 0.407239 -1.01
60 294 2p6r (A) 19 223 32.00 0.000000012 1 0.288229 0.28
640 892 4buj (E) 627 1177 27.00 0.0023 1 0.241793 1.09
640 873 4a4z (A) 627 903 29.00 0.00048 1 0.32442 0.91
1024 1207 4uos (A) 2 183 9.00 0.032 0.01 0.267567 -0.86
43 367 2zj2 (A) 3 291 24.00 0 1 0.289058 0.6
639 891 4buj (E) 627 1177 27.00 0.0032 1 0.236758 1.14
639 872 4a4z (A) 627 903 29.00 0.00067 1 0.317374 0.98
1044 1224 4uos (A) 2 182 11.00 0.027 0.05 0.259259 -0.78

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, gametocyte, early schizont, early trophozoite, late schizont, Sporozoite, Female 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 - 16 hs, early ring, late ring, late trophozoite, Male Gametocyte. Otto TD PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, Oocyst, Ring. Otto TD Zanghi G
Show/Hide expression data references
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • 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.
  • 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_159096)

Species Accession Gene Product
Plasmodium berghei PBANKA_1019100   DEAD/DEAH box helicase, putative
Plasmodium falciparum PF3D7_1425400   DEAD/DEAH box helicase, putative
Plasmodium knowlesi PKNH_1333200   DEAD/DEAH box helicase, putative
Plasmodium vivax PVX_085255   DEAD/DEAH box helicase, putative
Plasmodium yoelii PY06824   DNA helicase

Essentiality

PF3D7_1425400 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_1019100 Plasmodium berghei Dispensable plasmo
Show/Hide essentiality data references
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • 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
  • 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.
  • 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
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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): 0.6

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

15 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

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Gene identifier PF3D7_1425400 (Plasmodium falciparum), DEAD/DEAH box helicase, putative
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