Detailed view for LmjF.34.0860

Basic information

TDR Targets ID: 23466
Leishmania major, 60S ribosomal protein L13a, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 11.3355 | Length (AA): 222 | MW (Da): 25435 | Paralog Number: 1

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:0015934   large ribosomal subunit  
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 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
25 168 1vq8 (J) 10 143 32.00 0 0.99 1.05 -0.64
26 168 1j3a (A) 3 142 33.00 0.00000000015 1 0.97 -0.23
25 167 1vq8 (J) 10 142 29.00 0.000000000006 1 0.984644 -0.33

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 amastigotes, metacyclic. Fernandes MC
Show/Hide expression data references
  • Fernandes MC Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures.

Orthologs

Ortholog group members (OG5_126957)

Species Accession Gene Product
Arabidopsis thaliana AT3G24830   60S ribosomal protein L13a-2
Arabidopsis thaliana AT3G07110   60S ribosomal protein L13a-1
Arabidopsis thaliana AT4G13170   60S ribosomal protein L13a-3
Arabidopsis thaliana AT5G48760   60S ribosomal protein L13a-4
Babesia bovis BBOV_II002800   ribosomal protein L13, putative
Brugia malayi Bm1_33290   60S ribosomal protein L13a
Candida albicans CaO19.6085   likely cytosolic ribosomal protein similar to S. cerevisiae RPL16A (YIL133C) large subunit protein L16
Candida albicans CaO19.13504   likely cytosolic ribosomal protein similar to S. cerevisiae RPL16A (YIL133C) large subunit protein L16
Caenorhabditis elegans CELE_M01F1.2   Protein RPL-16
Cryptosporidium hominis Chro.50290   60S ribosomal protein L13a
Cryptosporidium parvum cgd5_970   60S ribosomal protein L13A
Dictyostelium discoideum DDB_G0275881   S60 ribosomal protein L13a
Drosophila melanogaster Dmel_CG1475   Ribosomal protein L13A
Echinococcus granulosus EgrG_000423900   ribosomal protein rpl13a
Entamoeba histolytica EHI_095610   ribosomal protein L13, putative
Entamoeba histolytica EHI_017700   ribosomal protein L13, putative
Entamoeba histolytica EHI_114400   ribosomal protein L13, putative
Entamoeba histolytica EHI_200090   ribosomal protein L13A, putative
Entamoeba histolytica EHI_099730   ribosomal protein L13, putative
Echinococcus multilocularis EmuJ_000423900   ribosomal protein rpl13a
Giardia lamblia GL50803_11247   Ribosomal protein L13a
Homo sapiens ENSG00000142541   ribosomal protein L13a
Leishmania braziliensis LbrM.20.0830   60S ribosomal protein L13a, putative
Leishmania braziliensis LbrM.15.0210   60S ribosomal protein L13a, putative
Leishmania infantum LinJ.34.0910   60S ribosomal protein L13a, putative
Leishmania infantum LinJ.15.0220   60S ribosomal protein L13a, putative
Leishmania major LmjF.34.0860   60S ribosomal protein L13a, putative
Leishmania major LmjF.15.0200   60S ribosomal protein L13a, putative
Leishmania mexicana LmxM.33.0860   60S ribosomal protein L13a, putative
Leishmania mexicana LmxM.15.0200   60S ribosomal protein L13a, putative
Loa Loa (eye worm) LOAG_07738   60S ribosomal protein L13a
Mus musculus 102642840   60S ribosomal protein L13a-like
Mus musculus ENSMUSG00000074129   ribosomal protein L13A
Neospora caninum NCLIV_043330   hypothetical protein
Oryza sativa 4342219   Os07g0109500
Oryza sativa 4334152   Os03g0755700
Oryza sativa 4334154   Os03g0756000
Plasmodium berghei PBANKA_1202400   60S ribosomal protein L13, putative
Plasmodium falciparum PF3D7_1004000   60S ribosomal protein L13, putative
Plasmodium knowlesi PKNH_0802800   60S ribosomal protein L13, putative
Plasmodium vivax PVX_094400   60S ribosomal protein L13a, putative
Plasmodium yoelii PY07370   ribosomal protein L13, putative
Saccharomyces cerevisiae YNL069C   ribosomal 60S subunit protein L16B
Saccharomyces cerevisiae YIL133C   ribosomal 60S subunit protein L16A
Schistosoma japonicum Sjp_0099250   60S ribosomal protein L13a, putative
Schistosoma japonicum Sjp_0311630   ko:K02872 large subunit ribosomal protein L13Ae, putative
Schistosoma mansoni Smp_090230   60S ribosomal protein L13a
Schmidtea mediterranea mk4.003384.05  
Schmidtea mediterranea mk4.009926.00   60S ribosomal protein L13a
Schmidtea mediterranea mk4.024192.02  
Trypanosoma brucei gambiense Tbg972.4.3550   60S ribosomal protein L13a, putative
Trypanosoma brucei gambiense Tbg972.5.2220   60S ribosomal protein L13a, putative
Trypanosoma brucei Tb927.4.3550   60S ribosomal protein L13a, putative
Trypanosoma brucei Tb927.5.1610   60S ribosomal protein L13a, putative
Trypanosoma congolense TcIL3000_0_20590   60S ribosomal protein L13a, putative
Trypanosoma cruzi TcCLB.507673.20   60S ribosomal protein L13a, putative
Trypanosoma cruzi TcCLB.506201.20   60S ribosomal protein L13a, putative
Trypanosoma cruzi TcCLB.506315.50   60S ribosomal protein L13a, putative
Trypanosoma cruzi TcCLB.506739.150   60S ribosomal protein L13a, putative
Toxoplasma gondii TGME49_292130   ribosomal protein RPL13A
Theileria parva TP04_0388   60S ribosomal protein L13, putative
Trichomonas vaginalis TVAG_484060   ribosomal protein L13, putative
Trichomonas vaginalis TVAG_447820   ribosomal protein L13, putative
Trichomonas vaginalis TVAG_026230   ribosomal protein L13, putative
Trichomonas vaginalis TVAG_110890   60S ribosomal protein L13a, putative
Trichomonas vaginalis TVAG_070530   ribosomal protein L13, putative
Trichomonas vaginalis TVAG_434650   60S ribosomal protein L13a, putative
Trichomonas vaginalis TVAG_344720   60S ribosomal protein L13a, putative

Essentiality

LmjF.34.0860 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.5.1610 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.5.1610 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.5.1610 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.5.1610 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Tb927.4.3550 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.3550 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.4.3550 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.4.3550 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_M01F1.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_M01F1.2 Caenorhabditis elegans larval arrest wormbase
CELE_M01F1.2 Caenorhabditis elegans slow growth wormbase
PBANKA_1202400 Plasmodium berghei Essential plasmo
TGME49_292130 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • 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

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

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier LmjF.34.0860 (Leishmania major), 60S ribosomal protein L13a, putative
Title for this comment
Comment