Detailed view for Rv2909c

Basic information

TDR Targets ID: 7088
Mycobacterium tuberculosis, 30S ribosomal protein S16 RpsP
Source Database / ID:  Tuberculist 

pI: 10.5675 | Length (AA): 162 | MW (Da): 17437 | 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

PF00886   Ribosomal protein S16

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 is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
3 82 2vqe (P) 2 82 51.00 0 1 1.23093 -1.62

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

Orthologs

Ortholog group members (OG5_127603)

Species Accession Gene Product
Arabidopsis thaliana ArthCp004   ribosomal protein S16
Arabidopsis thaliana AT5G56940   ribosomal protein S16 family protein
Arabidopsis thaliana AT4G34620   small subunit ribosomal protein 16
Brugia malayi Bm1_43310   28S ribosomal protein S16, mitochondrial precursor, putative
Candida albicans CaO19.7012   likely mitochondrial ribosomal protein similar to S. cerevisiae MRPS16 (YPL013C) small subunit protein S16
Candida albicans CaO19_7012   hypothetical protein
Caenorhabditis elegans CELE_F56D1.3   Protein MRPS-16
Chlamydia trachomatis CT_026   30S ribosomal protein S16
Drosophila melanogaster Dmel_CG8338   mitochondrial ribosomal protein S16
Escherichia coli b2609   30S ribosomal subunit protein S16
Echinococcus granulosus EgrG_000576000   28S ribosomal protein S16
Echinococcus multilocularis EmuJ_000576000   28S ribosomal protein S16
Homo sapiens ENSG00000182180   mitochondrial ribosomal protein S16
Loa Loa (eye worm) LOAG_10356   28S ribosomal protein S16
Mycobacterium leprae ML1618c   PROBABLE 30S RIBOSOMAL PROTEIN S16 RPSP
Mus musculus ENSMUSG00000049960   mitochondrial ribosomal protein S16
Mycobacterium tuberculosis Rv2909c   30S ribosomal protein S16 RpsP
Mycobacterium ulcerans MUL_2047   30S ribosomal protein S16
Oryza sativa 3131439   ribosomal protein S16
Oryza sativa 4346044   Os08g0517900
Oryza sativa 4347467   Os09g0498100
Saccharomyces cerevisiae YPL013C   mitochondrial 37S ribosomal protein MRPS16
Schistosoma japonicum Sjp_0216120   Probable mitochondrial 28S ribosomal protein S16, putative
Schistosoma mansoni Smp_066480   28S ribosomal protein S16
Schmidtea mediterranea mk4.031738.02  
Schmidtea mediterranea mk4.001309.00   Probable 28S ribosomal protein S16, mitochondrial
Treponema pallidum TP0905   ribosomal protein S16 (rpsP)
Wolbachia endosymbiont of Brugia malayi Wbm0531   30S ribosomal protein S16

Essentiality

Rv2909c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2956 this record Mycobacterium tuberculosis non-essential nmpdr
b2609 Escherichia coli essential goodall
CELE_F56D1.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_F56D1.3 Caenorhabditis elegans slow growth wormbase
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • 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

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 Rv2909c (Mycobacterium tuberculosis), 30S ribosomal protein S16 RpsP
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