Detailed view for Rv1642

Basic information

TDR Targets ID: 7066
Mycobacterium tuberculosis, 50S ribosomal protein L35 RpmI
Source Database / ID:  Tuberculist 

pI: 12.7562 | Length (AA): 64 | MW (Da): 7220 | 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

PF01632   Ribosomal protein L35

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 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 63 5dm6 (3) 2 63 34.00 0 0.92 1.41595 -0.23
2 61 4wfa (3) 2 61 42.00 0.00000000042 0.03 1.2668 0.78

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:

PDB tag
  • 5V7Q:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5V93:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Lower 20-40% 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_130370)

Species Accession Gene Product
Arabidopsis thaliana AT2G24090   ribosomal protein L35
Babesia bovis BBOV_IV005880   ribosomal protein L35, putative
Chlamydia trachomatis CT_834   50S ribosomal protein L35
Escherichia coli b1717   50S ribosomal subunit protein L35
Mycobacterium leprae ML1395   Probable 50S ribosomal protein L35 RpmI
Mycobacterium tuberculosis Rv1642   50S ribosomal protein L35 RpmI
Mycobacterium ulcerans MUL_1628   50S ribosomal protein L35
Oryza sativa 4341664   Os06g0647100
Plasmodium berghei PBANKA_0809200   ribosomal protein L35, putative
Plasmodium falciparum PF3D7_0907800   apicoplast ribosomal protein L35 precursor, putative
Plasmodium knowlesi PKNH_0705600   50s ribosomal protein l35, putative
Plasmodium vivax PVX_098835   ribosomal protein L35, putative
Plasmodium yoelii PY01737   ribosomal protein L35, putative
Schmidtea mediterranea mk4.039025.01  
Toxoplasma gondii TGME49_285530   ribosomal protein RPL35
Treponema pallidum TP0849   50S ribosomal protein L35
Theileria parva TP01_0393   hypothetical protein
Wolbachia endosymbiont of Brugia malayi Wbm0658   50S ribosomal protein L35

Essentiality

Rv1642 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b1717 Escherichia coli essential goodall
PBANKA_0809200 Plasmodium berghei Essential plasmo
TGME49_285530 Toxoplasma gondii Probably essential sidik
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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.

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 Rv1642 (Mycobacterium tuberculosis), 50S ribosomal protein L35 RpmI
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