Detailed view for PVX_000985

Basic information

TDR Targets ID: 268917
Plasmodium vivax, protein transport protein Sec24B, putative
Source Database / ID:  PlasmoDB 

pI: 6.5668 | Length (AA): 1554 | MW (Da): 170640 | 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

PF04811   Sec23/Sec24 trunk domain
PF04815   Sec23/Sec24 helical domain
PF08033   Sec23/Sec24 beta-sandwich domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0030127   COPII vesicle coat  
GO:0005515   protein binding  
GO:0006888   ER to Golgi vesicle-mediated transport  
GO:0006886   intracellular protein transport  

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
831 1522 1m2o (A) 6 724 16.00 0 1 0.63 -0.7
946 1549 1pcx (A) 303 926 25.00 0 1 0.67 -1.04
6 46 1nay (A) 106 146 15.00 0.46 0.01 0.225884 -0.68
818 1552 3efo (B) 300 1033 21.00 0 1 0.683473 -0.1
827 1552 3eh2 (A) 43 767 21.00 0 1 0.670681 -0.13
864 1549 3eh1 (A) 586 1268 21.00 0 1 0.669941 -0.08

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 60-80% percentile intraerythrocytic - 6 hs, intraerythrocytic - 12 hs, intraerythrocytic - 18 hs, intraerythrocytic - 24 hs, intraerythrocytic - 30 hs, intraerythrocytic - 36 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intraerythrocytic - 40 hs, intraerythrocytic - 48 hs. Zhu L
Show/Hide expression data references
  • Zhu L New insights into the Plasmodium vivax transcriptome using RNA-Seq.

Orthologs

Ortholog group members (OG5_139980)

Species Accession Gene Product
Babesia bovis BBOV_IV005730   conserved hypothetical protein
Cryptosporidium hominis Chro.80148   SEC24
Cryptosporidium parvum cgd8_1250   SEC24C-like component of COPII coatamer of ER-golgi vesicles
Neospora caninum NCLIV_046450   sec23/Sec24 helical domain-containing protein, putative
Plasmodium berghei PBANKA_1002800   protein transport protein Sec24B, putative
Plasmodium falciparum PF3D7_0405100   protein transport protein Sec24B
Plasmodium knowlesi PKNH_0303200   protein transport protein Sec24B, putative
Plasmodium vivax PVX_000985   protein transport protein Sec24B, putative
Plasmodium yoelii PY03895   putative Sec24-like protein
Toxoplasma gondii TGME49_226510   Sec23/Sec24 trunk domain-containing protein
Theileria parva TP01_0373   hypothetical protein

Essentiality

PVX_000985 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
TGME49_226510 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.

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 PVX_000985 (Plasmodium vivax), protein transport protein Sec24B, putative
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