Detailed view for Rv1015c

Basic information

TDR Targets ID: 7055
Mycobacterium tuberculosis, 50S ribosomal protein L25 RplY
Source Database / ID:  Tuberculist 

pI: 4.5632 | Length (AA): 215 | MW (Da): 22441 | 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

PF01386   Ribosomal L25p family
PF14693   Ribosomal protein TL5, C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005840   ribosome  
GO:0005622   intracellular  
GO:0008097   5S 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
6 95 1dfu (P) 1 91 33.00 0 0.52 0.808905 -0.26
8 191 1feu (A) 4 185 25.00 0 1 1.10271 0.14
8 98 5izn (A) 2 92 34.00 0 0.15 0.681156 0.64

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 60-80% percentile Dormant phase, Dormant phase. hasan 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_131263)

Species Accession Gene Product
Arabidopsis thaliana AT4G23620   ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain-containing protein
Arabidopsis thaliana AT5G66860   ribosomal protein L25/Gln-tRNA synthetase
Chlamydia trachomatis CT_799   50S ribosomal protein L25
Escherichia coli b2185   50S ribosomal subunit protein L25
Mycobacterium leprae ML0245c   Probable 50S ribosomal protein L25 RplY
Mycobacterium tuberculosis Rv1015c   50S ribosomal protein L25 RplY
Mycobacterium ulcerans MUL_4643   50S ribosomal protein L25/general stress protein Ctc
Oryza sativa 4326383   Os01g0593500
Oryza sativa 4338257   Os05g0270000
Oryza sativa 9272292   Os03g0612600
Treponema pallidum TP0372   50S ribosomal protein L25
Wolbachia endosymbiont of Brugia malayi Wbm0092   50S ribosomal protein L25

Essentiality

Rv1015c has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b2185 Escherichia coli essential goodall
Show/Hide essentiality data references
  • 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
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

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 Rv1015c (Mycobacterium tuberculosis), 50S ribosomal protein L25 RplY
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