Detailed view for PBANKA_0802300

Basic information

TDR Targets ID: 827895
Plasmodium berghei, E3 ubiquitin-protein ligase, putative
Source Database / ID: 

pI: 7.9992 | Length (AA): 3439 | MW (Da): 405312 | 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

PF00632   HECT-domain (ubiquitin-transferase)

Gene Ontology

Mouse over links to read term descriptions.
GO:0005488   binding  
GO:0004842   ubiquitin-protein ligase activity  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 10 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
132 171 1qgk (B) 15 54 15.00 0.45 0 0.369431 -2.3
426 1773 5kk5 (A) 8 1285 16.00 0 1 0.106174 1.62
948 1206 5t8u (A) 118 359 32.00 0.54 0.34 -0.134987 1.93
2716 2894 4uos (A) 1 183 16.00 0.18 0.12 0.32585 -1.54
2993 3433 5tj7 (A) 336 865 20.00 0 1 0.358035 -0.02
3072 3434 5c7m (A) 539 899 23.00 0 1 0.388354 -0.15
3166 3431 5c7m (A) 636 896 30.00 0.0000000000064 1 0.399048 -0.33
3167 3439 5lp8 (B) 4106 4374 34.00 0.000000000025 1 0.320084 0.38
3168 3429 1c4z (A) 589 843 34.00 0 1 0.391885 0.03
3351 3429 3pt3 (A) 2713 2791 28.00 0.0016 0.94 0.321772 -1.17

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 16 hs Trophozoite. Otto TD
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile 4 hs Ring, Erthyrocytic stages, Female gametocyte, Male gametocyte. Otto TD Yeoh LM
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Gametocyte, Ookinete, 22 hs Schizont. Otto TD
Show/Hide expression data references
  • Yeoh LM Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates.
  • Otto TD A comprehensive evaluation of rodent malaria parasite genomes and gene expression.

Orthologs

Ortholog group members (OG5_156983)

Species Accession Gene Product
Plasmodium berghei PBANKA_0802300   E3 ubiquitin-protein ligase, putative
Plasmodium falciparum PF3D7_0704600   E3 ubiquitin-protein ligase
Plasmodium knowlesi PKNH_0103100   E3 ubiquitin-protein ligase, putative
Plasmodium vivax PVX_087775   E3 ubiquitin-protein ligase, putative
Plasmodium yoelii PY06114   hypothetical protein
Plasmodium yoelii PY05241   putative ubiquitin fusion degradation protein
Plasmodium yoelii PY06762   CCAAT-box DNA binding protein subunit B

Essentiality

PBANKA_0802300 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
PBANKA_0802300 this record Plasmodium berghei Essential plasmo
Show/Hide essentiality data references
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84

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_0802300 (Plasmodium berghei), E3 ubiquitin-protein ligase, putative
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