Detailed view for PBANKA_1300700

Basic information

TDR Targets ID: 826513
Plasmodium berghei, LCCL domain-containing protein
Source Database / ID: 

pI: 4.8413 | Length (AA): 1615 | MW (Da): 183694 | 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

PF00754   F5/8 type C domain
PF03815   LCCL domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0062023   GO:collagen-containing extracellular matrix  

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
303 433 2w1s (A) 807 943 16.00 0 0.96 0.171815 -0.76
751 846 1jbi (A) 4 90 44.00 0.000035 1 0.448843 0.43
783 1610 3s4w (B) 153 1131 14.00 0 0.33 0.438394 1
834 1602 1h2v (C) 33 773 12.00 0 0.8 0.397861 0.77
905 1557 4n5c (D) 15 654 13.00 0 0.83 0.385034 0.71
1081 1217 4b1m (A) 543 675 23.00 0 1 0.31853 -0.58

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 Gametocyte, 22 hs Schizont, Male gametocyte. Otto TD Yeoh LM
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Ookinete, 4 hs Ring, Erthyrocytic stages, Female gametocyte. Otto TD Yeoh LM
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile 16 hs Trophozoite. 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_139606)

Species Accession Gene Product
Babesia bovis BBOV_III006360   LCCL domain containing protein
Cryptosporidium hominis Chro.70203   A135 protein
Cryptosporidium parvum cgd7_1730   CpCCp1/Cpa135
Neospora caninum NCLIV_048780   LCCL domain containing protein, related
Neospora caninum NCLIV_024000   hypothetical protein
Plasmodium berghei PBANKA_1300700   LCCL domain-containing protein
Plasmodium falciparum PF3D7_1475500   LCCL domain-containing protein
Plasmodium knowlesi PKNH_1245800   LCCL domain-containing protein
Plasmodium vivax PVX_118650   LCCL domain-containing protein
Plasmodium yoelii PY05554   LCCL domain-containing protein CCP2
Toxoplasma gondii TGME49_264070   F5/8 type C domain-containing protein
Toxoplasma gondii TGME49_223700   F5/8 type C domain-containing protein
Toxoplasma gondii TGME49_264075   hypothetical protein
Theileria parva TP02_0326   hypothetical protein

Essentiality

PBANKA_1300700 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
PBANKA_1300700 this record Plasmodium berghei Dispensable plasmo
TGME49_264070 Toxoplasma gondii Essentiality uncertain sidik
TGME49_223700 Toxoplasma gondii Essentiality uncertain sidik
TGME49_264075 Toxoplasma gondii Essentiality uncertain sidik
TGME49_264070 Toxoplasma gondii Probably non-essential sidik
TGME49_223700 Toxoplasma gondii Probably non-essential sidik
TGME49_264075 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

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_1300700 (Plasmodium berghei), LCCL domain-containing protein
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