Detailed view for PF3D7_0909900

Basic information

TDR Targets ID: 4774
Plasmodium falciparum, helicase SKI2W, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 6.9679 | Length (AA): 1373 | MW (Da): 160373 | 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
PF08148   DSHCT (NUC185) domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0003724   RNA helicase activity  
GO:0008026   ATP-dependent helicase activity  
GO:0005524   ATP binding  
GO:0004386   helicase activity  
GO:0003723   RNA binding  
GO:0003676   nucleic acid binding  
GO:0006401   RNA catabolic process  

Metabolic Pathways

Purine metabolism (KEGG)
RNA degradation (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
270 468 2g9n (A) 23 236 20.00 0.0000000000094 0.96 0.44 -1.32
280 449 1vec (A) 86 270 21.00 0 0.73 0.47 -1.69
5 174 4v3d (C) 518 716 15.00 0.82 0.03 0.288016 -0.55
234 1372 2xgj (A) 82 1073 30.00 0 1 0.91737 1.05
274 1372 4a4z (A) 299 1287 40.00 0 1 0.909937 1.02
298 1372 4u4c (A) 146 1073 37.00 0 1 0.938457 0.76
302 476 3ly5 (A) 202 384 27.00 0.075 0.99 0.328958 -0.21
318 860 4bgd (A) 516 989 28.00 0.000000000017 1 0.268984 1.28
668 758 3rc3 (A) 376 476 34.00 0.77 0.8 0.290778 0.67
76 403 4dkj (A) 61 393 29.00 0.39 0.37 0.101067 1.77
234 1371 2xgj (A) 82 1073 29.00 0 1 0.906046 1.04
274 1371 4a4z (A) 299 1287 40.00 0 1 0.918292 1.04
282 1371 4u4c (A) 130 1073 31.00 0 1 0.895061 0.8
1142 1361 4tql (A) 11 231 6.00 0.86 0.02 0.21235 -0.35

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 - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, Ring. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Oocyst, Sporozoite. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Female Gametocyte, Male Gametocyte. Lasonder E
Show/Hide expression data references
  • 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.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.

Orthologs

Ortholog group members (OG5_128384)

Species Accession Gene Product
Arabidopsis thaliana AT3G46960   DExD/H box RNA helicase
Babesia bovis BBOV_II002350   helicase with zinc finger motif protein, putative
Brugia malayi Bm1_22815   helicase
Candida albicans CaO19.6425   antiviral protein, blocks translation of non-poly(A) mRNAs
Candida albicans CaO19.13783   antiviral protein, blocks translation of non-poly(A) mRNAs
Caenorhabditis elegans CELE_F01G4.3   Protein SKIH-2
Cryptosporidium hominis Chro.30042   DEAD/DEAH box helicase
Cryptosporidium parvum cgd3_280   mRNA translation inhibitor SKI2 SFII helicase, DEXDc+HELICc
Dictyostelium discoideum DDB_G0277211   DEAD/DEAH box helicase
Drosophila melanogaster Dmel_CG10210   twister
Echinococcus granulosus EgrG_000462500   DNA RNA helicase C terminal
Entamoeba histolytica EHI_125170   DEAD/DEAH box helicase, putative
Echinococcus multilocularis EmuJ_000462500   DNA RNA helicase, C terminal
Homo sapiens ENSG00000204351   superkiller viralicidic activity 2-like (S. cerevisiae)
Loa Loa (eye worm) LOAG_15949   hypothetical protein
Loa Loa (eye worm) LOAG_13439   hypothetical protein
Loa Loa (eye worm) LOAG_05800   helicase
Loa Loa (eye worm) LOAG_14285   hypothetical protein
Mus musculus ENSMUSG00000040356   superkiller viralicidic activity 2-like (S. cerevisiae)
Neospora caninum NCLIV_014710   DEAD/DEAH box helicase domain-containing protein, putative
Plasmodium berghei PBANKA_0811100   helicase SKI2W, putative
Plasmodium falciparum PF3D7_0909900   helicase SKI2W, putative
Plasmodium knowlesi PKNH_0707900   helicase SKI2W, putative
Plasmodium vivax PVX_098935   DEAD/DEAH box helicase, putative
Plasmodium yoelii PY03503   antiviral protein ski2
Saccharomyces cerevisiae YLR398C   SKI complex RNA helicase subunit SKI2
Schistosoma japonicum Sjp_0009140   expressed protein
Schistosoma mansoni Smp_137580   helicase
Schmidtea mediterranea mk4.002322.00   Helicase SKI2W
Schmidtea mediterranea mk4.009203.00   Uncharacterized helicase
Schmidtea mediterranea mk4.024587.00   Helicase SKI2W
Toxoplasma gondii TGME49_285660   DEAD/DEAH box helicase domain-containing protein
Theileria parva TP04_0364   hypothetical protein
Trichomonas vaginalis TVAG_432490   activating signal cointegrator 1 complex subunit 3, helc1, putative
Trichomonas vaginalis TVAG_177450   helicase, putative

Essentiality

PF3D7_0909900 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_0811100 Plasmodium berghei Dispensable plasmo
TGME49_285660 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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

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_0909900 (Plasmodium falciparum), helicase SKI2W, putative
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