Detailed view for Rv2890c

Basic information

TDR Targets ID: 7073
Mycobacterium tuberculosis, 30S ribosomal protein S2 RpsB
Source Database / ID:  Tuberculist 

pI: 6.3591 | Length (AA): 287 | MW (Da): 31089 | 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

PF00318   Ribosomal protein S2

Gene Ontology

Mouse over links to read term descriptions.
GO:0005622   intracellular  
GO:0015935   small ribosomal subunit  
GO:0005840   ribosome  
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
2 285 4toi (A) 2 291 44.00 0 1 1.58055 -0.68
3 265 1i94 (B) 4 250 53.00 0 1 1.39538 0.84

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 20-40% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Dormant phase. murphy
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_128046)

Species Accession Gene Product
Arabidopsis thaliana AT3G03600   ribosomal protein S2
Arabidopsis thaliana ArthCp011   30S ribosomal protein S2
Brugia malayi Bm1_34650   28S ribosomal protein S2, mitochondrial
Candida albicans CaO19.5747   likely mitochondrial ribosomal protein similar to S. cerevisiae MRP4 (YHL004W) small subunit protein (E. coli S2)
Candida albicans CaO19.13170   likely mitochondrial ribosomal protein similar to S. cerevisiae MRP4 (YHL004W) small subunit protein (E. coli S2)
Caenorhabditis elegans CELE_T23B12.3   Protein MRPS-2
Chlamydia trachomatis CT_680   30S ribosomal protein S2
Dictyostelium discoideum DidioMp40   ribosomal protein S2
Drosophila melanogaster Dmel_CG2937   mitochondrial ribosomal protein S2
Escherichia coli b0169   30S ribosomal subunit protein S2
Echinococcus granulosus EgrG_000631300   28S ribosomal protein S2 mitochondrial
Echinococcus multilocularis EmuJ_000631300   28S ribosomal protein S2, mitochondrial
Homo sapiens ENSG00000122140   mitochondrial ribosomal protein S2
Loa Loa (eye worm) LOAG_05099   28S ribosomal protein S2
Mycobacterium leprae ML1598c   PROBABLE 30S RIBOSOMAL PROTEIN S2 RPSB
Mus musculus ENSMUSG00000035772   mitochondrial ribosomal protein S2
Mycobacterium tuberculosis Rv2890c   30S ribosomal protein S2 RpsB
Mycobacterium ulcerans MUL_2067   30S ribosomal protein S2
Oryza sativa 3131442   30S ribosomal protein S2
Saccharomyces cerevisiae YHL004W   mitochondrial 37S ribosomal protein MRP4
Schistosoma japonicum Sjp_0304400   ko:K02967 small subunit ribosomal protein S2, putative
Schistosoma mansoni Smp_102840.1   30S ribosomal protein S2
Schmidtea mediterranea mk4.000070.14   28S ribosomal protein S2, mitochondrial
Treponema pallidum TP0606   30S ribosomal protein S2
Wolbachia endosymbiont of Brugia malayi Wbm0808   30S ribosomal protein S2

Essentiality

Rv2890c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2937 this record Mycobacterium tuberculosis essential nmpdr
b0169 Escherichia coli essential goodall
CELE_T23B12.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_T23B12.3 Caenorhabditis elegans larval arrest wormbase
CELE_T23B12.3 Caenorhabditis elegans slow growth wormbase
Show/Hide essentiality data references
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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.
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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

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): 0.5

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 Rv2890c (Mycobacterium tuberculosis), 30S ribosomal protein S2 RpsB
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