Detailed view for Tb927.3.3310

Basic information

TDR Targets ID: 11378
Trypanosoma brucei, 60S ribosomal protein L13, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 11.9779 | Length (AA): 218 | MW (Da): 25428 | Paralog Number: 1

Signal peptide: N | GPI Anchor: | 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

PF01294   Ribosomal protein L13e

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 2 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
68 192 4yxx (A) 59 173 29.00 0.84 0.09 0.689595 0.73
85 213 5cwi (A) 7 137 17.00 0.67 0.07 0.721343 -0.23

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:

PDB tag
  • 3ZF7:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Procyclic, Bloodstream Form. Siegel TN
Show/Hide expression data references
  • Siegel TN Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites.

Orthologs

Ortholog group members (OG5_127128)

Species Accession Gene Product
Arabidopsis thaliana AT3G49010   60S ribosomal protein L13-1
Arabidopsis thaliana AT5G23900   60S ribosomal protein L13-3
Arabidopsis thaliana AT3G48960   putative 60S ribosomal protein L13-2
Babesia bovis BBOV_IV005370   ribosomal protein L13, putative
Brugia malayi Bm1_47775   60S ribosomal protein L13
Candida albicans CaO19.10511   likely cytosolic ribosomal protein similar to S. cerevisiae RPL13A (YDL082W) and RPL13B (YMR142C) large subunit protein L13
Candida albicans CaO19.2994   likely cytosolic ribosomal protein similar to S. cerevisiae RPL13A (YDL082W) and RPL13B (YMR142C) large subunit protein L13
Caenorhabditis elegans CELE_C32E8.2   Protein RPL-13, isoform A
Cryptosporidium hominis Chro.20312   60S ribosomal protein L13
Cryptosporidium parvum cgd2_2990   60S ribosomal protein L13, putative
Dictyostelium discoideum DDB_G0291870   S60 ribosomal protein L13
Drosophila melanogaster Dmel_CG4651   Ribosomal protein L13
Echinococcus granulosus EgrG_000517800   ribosomal protein L13
Entamoeba histolytica EHI_181560   60S ribosomal protein L13, putative
Entamoeba histolytica EHI_187150   60S ribosomal protein L13, putative
Echinococcus multilocularis EmuJ_000517800   ribosomal protein L13
Giardia lamblia GL50803_14622   Ribosomal protein L13
Homo sapiens ENSG00000167526   ribosomal protein L13
Leishmania braziliensis LbrM.29.2440   60S ribosomal protein L13, putative
Leishmania braziliensis LbrM.29.2430   60S ribosomal protein L13, putative
Leishmania infantum LinJ.29.2570   60S ribosomal protein L13, putative
Leishmania infantum LinJ.29.2580   60S ribosomal protein L13, putative
Leishmania major LmjF.29.2460   60S ribosomal protein L13, putative
Leishmania major LmjF.29.2470   60S ribosomal protein L13, putative
Leishmania mexicana LmxM.08_29.2461   60S ribosomal protein L13, putative
Leishmania mexicana LmxM.08_29.2460   60S ribosomal protein L13, putative
Loa Loa (eye worm) LOAG_08453   60S ribosomal protein L13
Mus musculus ENSMUSG00000000740   ribosomal protein L13
Mus musculus 100040416   predicted gene 10071
Neospora caninum NCLIV_024870   hypothetical protein
Oryza sativa 4339923   Os06g0115500
Oryza sativa 4333306   Os03g0576700
Plasmodium berghei PBANKA_1423500   60S ribosomal protein L13-2, putative
Plasmodium falciparum PF3D7_0814000   60S ribosomal protein L13-2, putative
Plasmodium knowlesi PKNH_1426300   60S ribosomal protein L13, putative
Plasmodium vivax PVX_123070   60S ribosomal protein L13, putative
Plasmodium yoelii PY06465   Ribosomal protein L13e
Saccharomyces cerevisiae YMR142C   ribosomal 60S subunit protein L13B
Saccharomyces cerevisiae YDL082W   ribosomal 60S subunit protein L13A
Schistosoma japonicum Sjp_0093550   ko:K02873 large subunit ribosomal protein L13e, putative
Schistosoma mansoni Smp_022640   60S ribosomal protein L13
Schmidtea mediterranea mk4.000285.03  
Trypanosoma brucei gambiense Tbg972.3.3470   60S ribosomal protein L13, putative
Trypanosoma brucei gambiense Tbg972.3.3480   60S ribosomal protein L13, putative
Trypanosoma brucei Tb927.3.3320   60S ribosomal protein L13, putative
Trypanosoma brucei Tb927.3.3310   60S ribosomal protein L13, putative
Trypanosoma congolense TcIL3000_0_42440   60S ribosomal protein L13, putative
Trypanosoma cruzi TcCLB.508153.290   60S ribosomal protein L13, putative
Trypanosoma cruzi TcCLB.508153.280   60S ribosomal protein L13, putative
Trypanosoma cruzi TcCLB.510323.30   60S ribosomal protein L13, putative
Toxoplasma gondii TGME49_263050   ribosomal protein RPL13
Theileria parva TP01_0199   60S ribosomal protein L13e, putative
Trichomonas vaginalis TVAG_423320   60S ribosomal protein L13, putative
Trichomonas vaginalis TVAG_182520   60S ribosomal protein L13, putative
Trichomonas vaginalis TVAG_438370   60S ribosomal protein L13, putative
Trichomonas vaginalis TVAG_190280   60S ribosomal protein L13, putative
Trichomonas vaginalis TVAG_199380   60S ribosomal protein L13, putative
Trichomonas vaginalis TVAG_112230   60S ribosomal protein L13, putative

Essentiality

Tb927.3.3310 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.3.3310 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.3.3310 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.3.3310 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.3.3310 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C32E8.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_C32E8.2 Caenorhabditis elegans larval arrest wormbase
CELE_C32E8.2 Caenorhabditis elegans sterile wormbase
TGME49_263050 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) decreased (PATO:0000468) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: decreased cell proliferation (significant loss of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) decreased (PATO:0000468) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: decreased cell proliferation (significant loss of fitness) in differentiation of procyclic to bloodstream forms . References: 21363968

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

1 literature reference was collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier Tb927.3.3310 (Trypanosoma brucei), 60S ribosomal protein L13, putative
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