Detailed view for PBANKA_1457300

Basic information

TDR Targets ID: 828264
Plasmodium berghei, glucose inhibited division protein a homologue, putative
Source Database / ID: 

pI: 9.6629 | Length (AA): 937 | MW (Da): 107589 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 1

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

PF01134   Glucose inhibited division protein A
PF13932   GidA associated domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0050660   FAD binding  
GO:0008033   tRNA processing  
GO:0002098   tRNA wobble uridine modification  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 4 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
76 925 2zxi (A) 0 615 42.00 0 1 0.853951 1.17
85 137 3oz2 (A) 4 53 48.00 0.058 0.23 0.397464 0.92
632 763 1eku (A) 103 226 18.00 0.97 0.32 0.375775 -0.73
633 809 4uos (A) 7 184 16.00 0.0049 0.02 0.480701 -1.66

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
Mid 40-60% percentile 4 hs Ring, 16 hs Trophozoite, Erthyrocytic stages, Male gametocyte. Otto TD Yeoh LM
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Gametocyte, Ookinete, 22 hs Schizont, Female gametocyte. Otto TD Yeoh LM
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_127775)

Species Accession Gene Product
Arabidopsis thaliana AT2G13440   glucose-inhibited division family A protein
Babesia bovis BBOV_III003040   glucose inhibited division protein A family protein
Brugia malayi Bm1_42115   Hypothetical 71.7 kDa protein F52H3.2 in chromosome II, putative
Candida albicans CaO19.5050   similar to evolutionarily conserved MTO/gidA protein which is involved in the hypermodification of the wobble position of some t
Candida albicans CaO19.12517   similar to evolutionarily conserved MTO/gidA protein which is involved in the hypermodification of the wobble position of some t
Caenorhabditis elegans CELE_F52H3.2   Protein F52H3.2
Chlamydia trachomatis CT_498   tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
Dictyostelium discoideum DDB_G0289183   hypothetical protein
Drosophila melanogaster Dmel_CG4610   CG4610 gene product from transcript CG4610-RA
Escherichia coli b3741   5-methylaminomethyl-2-thiouridine modification at tRNA U34
Homo sapiens ENSG00000135297   mitochondrial tRNA translation optimization 1
Loa Loa (eye worm) LOAG_12795   glucose inhibited division protein A
Loa Loa (eye worm) LOAG_07910   glucose inhibited division protein A
Mus musculus ENSMUSG00000032342   mitochondrial translation optimization 1 homolog (S. cerevisiae)
Neospora caninum NCLIV_017330   tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA, related
Oryza sativa 4325242   Os01g0960300
Onchocerca volvulus OVOC10804  
Plasmodium berghei PBANKA_1457300   glucose inhibited division protein a homologue, putative
Plasmodium falciparum PF3D7_1244000   glucose inhibited division protein a homologue, putative
Plasmodium knowlesi PKNH_1463300   glucose inhibited division protein a homologue, putative
Plasmodium yoelii PY01214   Glucose inhibited division protein A
Saccharomyces cerevisiae YGL236C   Mto1p
Schmidtea mediterranea mk4.064901.00  
Toxoplasma gondii TGME49_242010   glucose inhibited division protein A subfamily protein
Treponema pallidum TP0044   tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA
Theileria parva TP04_0141   glucose inhibited division protein A, putative
Wolbachia endosymbiont of Brugia malayi Wbm0611   tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA

Essentiality

PBANKA_1457300 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
b3741 Escherichia coli non-essential goodall
CELE_F52H3.2 Caenorhabditis elegans embryonic arrest wormbase
CELE_F52H3.2 Caenorhabditis elegans larval arrest wormbase
YGL236C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1457300 this record Plasmodium berghei Essential plasmo
TGME49_242010 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

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_1457300 (Plasmodium berghei), glucose inhibited division protein a homologue, putative
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