Detailed view for PVX_002825

Basic information

TDR Targets ID: 265349
Plasmodium vivax, 50S ribosomal protein L13, putative
Source Database / ID:  PlasmoDB 

pI: 11.0153 | Length (AA): 212 | MW (Da): 24176 | 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

PF00572   Ribosomal protein L13

Gene Ontology

Mouse over links to read term descriptions.
GO:0005840   ribosome  
GO:0005622   intracellular  
GO:0003735   structural constituent of ribosome  
GO:0006412   translation  

Metabolic Pathways

Ribosome (KEGG)

Structural information

Modbase 3D models:

There are 5 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
62 191 1nkw (H) 37 166 35.00 0 0.94 0.96 0.73
67 211 1j3a (A) 2 131 21.00 0 0.77 0.66 -0.48
25 78 3tny (A) 176 229 35.00 0.29 0.12 0.518117 0.94
51 193 4wfa (G) 1 142 32.00 0 1 1.03963 -0.02
53 197 5dm6 (G) 30 171 30.00 0 1 1.05406 -0.41

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. Zhu L
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intraerythrocytic - 30 hs, intraerythrocytic - 36 hs, intraerythrocytic - 48 hs. Zhu L
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intraerythrocytic - 40 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_127268)

Species Accession Gene Product
Arabidopsis thaliana AT3G01790   large subunit ribosomal protein L13
Arabidopsis thaliana AT1G78630   50S ribosomal protein L13
Babesia bovis BBOV_IV005700   50S ribosomal protein L13, putative
Candida albicans CaO19.10856   likely mitochondrial ribosomal protein similar to S. cerevisiae MRPL23 (YOR150W) large subunit protein (E. coli L13)
Candida albicans CaO19.3348   likely mitochondrial ribosomal protein similar to S. cerevisiae MRPL23 (YOR150W) large subunit protein (E. coli L13)
Caenorhabditis elegans CELE_F13G3.11   Protein MRPL-13
Chlamydia trachomatis CT_125   50S ribosomal protein L13
Dictyostelium discoideum DDB_G0274959   hypothetical protein
Drosophila melanogaster Dmel_CG10603   mitochondrial ribosomal protein L13
Escherichia coli b3231   50S ribosomal subunit protein L13
Echinococcus granulosus EgrG_001032000   ribosomal protein L13
Echinococcus multilocularis EmuJ_001032000   ribosomal protein L13
Homo sapiens ENSG00000172172   mitochondrial ribosomal protein L13
Leishmania braziliensis LbrM.20.3270   50S ribosomal protein L13-like protein
Leishmania donovani LdBPK_343470.1   50S ribosomal protein L13-like protein
Leishmania infantum LinJ.34.3470   50S ribosomal protein L13-like protein
Leishmania major LmjF.34.3680   50S ribosomal protein L13-like protein
Leishmania mexicana LmxM.33.3680   50S ribosomal protein L13-like protein
Mycobacterium leprae ML0364   Probable 50S ribosomal protein L13 RplM
Mus musculus 68537   mitochondrial ribosomal protein L13
Mycobacterium tuberculosis Rv3443c   50S ribosomal protein L13 RplM
Mycobacterium ulcerans MUL_0864   50S ribosomal protein L13
Neospora caninum NCLIV_047460   50S ribosomal protein L13, putative
Oryza sativa 4325555   Os01g0749200
Oryza sativa 4338199   Os05g0243300
Plasmodium berghei PBANKA_0311100   mitochondrial large ribosomal subunit, putative
Plasmodium falciparum PF3D7_0214200   mitochondrial ribosomal protein L13 precursor, putative
Plasmodium knowlesi PKNH_0406600   ribosomal protein L13, putative
Plasmodium vivax PVX_002825   50S ribosomal protein L13, putative
Saccharomyces cerevisiae YOR150W   mitochondrial 54S ribosomal protein YmL23
Schistosoma japonicum Sjp_0202660   ko:K02871 large subunit ribosomal protein L13, putative
Schistosoma mansoni Smp_121790.1   50S ribosomal protein L13
Schmidtea mediterranea mk4.000263.07   39S ribosomal protein L13, mitochondrial
Trypanosoma brucei gambiense Tbg972.4.900   50S ribosomal protein L13, putative
Trypanosoma brucei Tb927.4.1070   Mitochondrial ribosomal protein L13
Trypanosoma congolense TcIL3000_4_690   50S ribosomal protein L13, putative
Trypanosoma cruzi TcCLB.503929.20   ribosomal protein L13, putative
Trypanosoma cruzi TcCLB.506405.110   ribosomal protein L13, putative
Toxoplasma gondii TGME49_225240   50S ribosomal protein L13, putative
Treponema pallidum TP1025   50S ribosomal protein L13
Theileria parva TP01_0369   60S ribosomal protein L13, putative
Wolbachia endosymbiont of Brugia malayi Wbm0574   50S ribosomal protein L13

Essentiality

PVX_002825 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.1070 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.4.1070 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.4.1070 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.4.1070 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b3231 Escherichia coli essential goodall
CELE_F13G3.11 Caenorhabditis elegans embryonic lethal wormbase
PBANKA_0311100 Plasmodium berghei Essential plasmo
TGME49_225240 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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

Druggability index (range: 0 to 1): 0.7

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_002825 (Plasmodium vivax), 50S ribosomal protein L13, putative
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