Detailed view for PF3D7_0503000

Basic information

TDR Targets ID: 4060
Plasmodium falciparum, 50S ribosomal protein L28, apicoplast, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 11.0369 | Length (AA): 262 | MW (Da): 31225 | Paralog Number: 0

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

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

PF00830   Ribosomal L28 family

Gene Ontology

Mouse over links to read term descriptions.
GO:0020011   apicoplast  
GO:0015934   large ribosomal subunit  
GO:0005840   ribosome  
GO:0005622   intracellular  
GO:0003735   structural constituent of ribosome  
GO:0006412   translation  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 3 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
140 183 4wfa (U) 14 55 31.00 0.000039 0.05 0.225939 2.11
194 261 3k29 (A) 93 160 13.00 0.2 0 0.488542 -1.05
212 261 1w9r (A) 55 104 14.00 0.97 0 0.48884 -1.64

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, early schizont, early trophozoite, late schizont, late trophozoite, Female Gametocyte, Male Gametocyte. PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, merozoite, sporozoite, late ring, Oocyst. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, early ring, Ring, Sporozoite. Otto TD PlasmoDB Zanghi G
Show/Hide expression data references
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • 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_130709)

Species Accession Gene Product
Arabidopsis thaliana AT2G33450   50S ribosomal protein L28
Babesia bovis BBOV_II007060   50S ribosomal subunit protein L28, putative
Chlamydia trachomatis CT_086   50S ribosomal protein L28
Escherichia coli b3637   50S ribosomal subunit protein L28
Mycobacterium tuberculosis Rv0105c   50S ribosomal protein L28-1 RpmB1
Mycobacterium tuberculosis Rv2058c   50S ribosomal protein L28 RpmB2
Mycobacterium ulcerans MUL_1983   50S ribosomal protein L28
Mycobacterium ulcerans MUL_4831   50S ribosomal protein L28
Neospora caninum NCLIV_003980   50S ribosomal protein L28, related
Oryza sativa 4337526   Os05g0101400
Plasmodium berghei PBANKA_1102700   50S ribosomal protein L28, apicoplast, putative
Plasmodium falciparum PF3D7_0503000   50S ribosomal protein L28, apicoplast, putative
Plasmodium knowlesi PKNH_1030900   50S ribosomal protein L28, apicoplast, putative
Plasmodium vivax PVX_097655   50S ribosomal protein L28, apicoplast, putative
Plasmodium yoelii PY04664   ribosomal protein L28, putative
Toxoplasma gondii TGME49_209710   ribosomal protein RPL28
Treponema pallidum TP0362   50S ribosomal protein L28
Theileria parva TP02_0680   60S ribosomal protein L28, putative

Essentiality

PF3D7_0503000 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu106 Mycobacterium tuberculosis non-essential nmpdr
b3637 Escherichia coli essential goodall
TGME49_209710 Toxoplasma gondii Probably essential 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • 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

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_0503000 (Plasmodium falciparum), 50S ribosomal protein L28, apicoplast, putative
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