Detailed view for Rv0708

Basic information

TDR Targets ID: 7046
Mycobacterium tuberculosis, 50S ribosomal protein L16 RplP
Source Database / ID:  Tuberculist 

pI: 11.737 | Length (AA): 138 | MW (Da): 15692 | Paralog Number: 0

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

PF00252   Ribosomal protein L16p/L10e

Gene Ontology

Mouse over links to read term descriptions.
GO:0005840   ribosome  
GO:0005622   intracellular  
GO:0019843   rRNA binding  
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
1 136 1wki (A) 1 136 56.00 0 1 1.60411 0.21
4 137 4wfa (J) 4 137 57.00 0 1 1.66761 -0.47
34 124 1jj2 (H) 48 152 22.00 0.41 0.99 0.95192 -0.5

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 Dormant phase. murphy
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Dormant phase. hasan
Show/Hide expression data references
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.

Orthologs

Ortholog group members (OG5_127517)

Species Accession Gene Product
Arabidopsis thaliana ArthMp008   ribosomal protein L16
Arabidopsis thaliana ArthCp060   ribosomal protein L16
Arabidopsis thaliana ArthMp009   ribosomal protein S3
Babesia bovis BBOV_V000410   rpl16
Babesia bovis BBOV_II005040   ribosomal protein L16, putative
Brugia malayi Bm1_03960   ribosomal protein L16 containing protein
Candida albicans CaO19.2019   likely mitochondrial ribosomal protein similar to S. cerevisiae MRPL16 (YBL038W) large subunit protein L16
Candida albicans CaO19.9569   likely mitochondrial ribosomal protein similar to S. cerevisiae MRPL16 (YBL038W) large subunit protein L16
Caenorhabditis elegans CELE_T04A8.11   Protein MRPL-16
Chlamydia trachomatis CT_521   50S ribosomal protein L16
Dictyostelium discoideum DidioMp28   ribosomal protein L16
Drosophila melanogaster Dmel_CG3109   mitochondrial ribosomal protein L16
Escherichia coli b3313   50S ribosomal subunit protein L16
Echinococcus granulosus EgrG_000978100   39S ribosomal protein L16 mitochondrial
Echinococcus multilocularis EmuJ_000978100   39S ribosomal protein L16, mitochondrial
Homo sapiens ENSG00000166902   mitochondrial ribosomal protein L16
Loa Loa (eye worm) LOAG_10621   ribosomal protein L16 containing protein
Mycobacterium leprae ML1856c   PROBABLE 50S RIBOSOMAL PROTEIN L16 RPLP
Mus musculus ENSMUSG00000024683   mitochondrial ribosomal protein L16
Mycobacterium tuberculosis Rv0708   50S ribosomal protein L16 RplP
Mycobacterium ulcerans MUL_0797   50S ribosomal protein L16
Neospora caninum NCLIV_012280   ribosomal protein L16, putative
Oryza sativa 3131423   ribosomal protein L16
Oryza sativa 4352371   Os12g0524700
Oryza sativa 6450196   ribosomal protein S3
Plasmodium berghei PBANKA_API00380   apicoplast ribosomal protein L16
Plasmodium berghei PBANKA_1037700   mitochondrial ribosomal protein L16 precursor, putative
Plasmodium falciparum PF3D7_1404400   mitochondrial ribosomal protein L16 precursor, putative
Plasmodium falciparum PF3D7_API01800   apicoplast ribosomal protein L16
Plasmodium knowlesi PKNH_1353700   ribosomal protein L16, putative
Plasmodium knowlesi PKNH_API02700   apicoplast ribosomal protein L16, putative
Plasmodium vivax PVX_086215   50S ribosomal protein L16, putative
Plasmodium yoelii PY04761   ribosomal protein L16, putative
Plasmodium yoelii PY00995   ribosomal protein L16, putative
Saccharomyces cerevisiae YBL038W   mitochondrial 54S ribosomal protein YmL47
Schistosoma japonicum Sjp_0048310   39S ribosomal protein L16, mitochondrial precursor, putative
Schistosoma mansoni Smp_154690   ribosomal protein related
Schmidtea mediterranea mk4.006620.01   39S ribosomal protein L16, mitochondrial
Toxoplasma gondii TGME49_300613   ribosomal protein L16, putative
Toxoplasma gondii TGME49_220150   50S ribosomal protein L16, putative
Treponema pallidum TP0196   50S ribosomal protein L16
Theileria parva TP04_0046   60S ribosomal protein L16, putative
Theileria parva TP05_0006   ribosomal protein L16, putative
Wolbachia endosymbiont of Brugia malayi Wbm0334   50S ribosomal protein L16

Essentiality

Rv0708 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu720 this record Mycobacterium tuberculosis essential nmpdr
b3313 Escherichia coli essential goodall
CELE_T04A8.11 Caenorhabditis elegans embryonic lethal wormbase
CELE_T04A8.11 Caenorhabditis elegans larval arrest wormbase
CELE_T04A8.11 Caenorhabditis elegans slow growth wormbase
PBANKA_1037700 Plasmodium berghei Essential plasmo
TGME49_220150 Toxoplasma gondii Probably essential sidik
TGME49_300613 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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.

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.

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User comments

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Gene identifier Rv0708 (Mycobacterium tuberculosis), 50S ribosomal protein L16 RplP
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