Detailed view for TP0576

Basic information

TDR Targets ID: 596508
Treponema pallidum, peptide chain release factor 2 (prfB)
Source Database / ID:  KEGG  

pI: 7.7288 | Length (AA): 368 | MW (Da): 41596 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | 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

PF00472   RF-1 domain
PF03462   PCRF domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0016149   translation release factor activity, codon specific  
GO:0005737   cytoplasm  
GO:0003747   translation release factor activity  
GO:0006415   translational termination  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
1 357 1gqe (A) 7 363 44.00 0 1 1.54571 -0.44
37 356 1zbt (A) 0 347 29.00 0 1 1.13477 0.07

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_130058)

Species Accession Gene Product
Arabidopsis thaliana AT1G56350   peptide chain release factor 2
Arabidopsis thaliana AT5G36170   protein high chlorophyll fluorescent 109
Babesia bovis BBOV_II003430   peptide chain release factor 2, putative
Brugia malayi Bm1_26875   peptide chain release factor 2, programmed
Chlamydia trachomatis CT_459   peptide chain release factor 2
Dictyostelium discoideum DDB_G0288835   class I peptide chain release factor
Escherichia coli b2891   peptide chain release factor RF-2
Mycobacterium leprae ML0667   Probable peptide chain release factor 2 PrfB (RF-2)
Mycobacterium tuberculosis Rv3105c   Probable peptide chain release factor 2 PrfB (RF-2)
Mycobacterium ulcerans MUL_2412   peptide chain release factor 2
Oryza sativa 4343528   Os07g0546600
Oryza sativa 4332598   Os03g0305700
Plasmodium berghei PBANKA_0802600   peptide chain release factor 2, putative
Plasmodium falciparum PF3D7_0704900   peptide chain release factor 2
Plasmodium knowlesi PKNH_0103400   peptide chain release factor 2, putative
Plasmodium vivax PVX_087790   peptide chain release factor, putative
Plasmodium yoelii PY04145   Peptidyl-tRNA hydrolase domain, putative
Schmidtea mediterranea mk4.061795.00   Probable peptide chain release factor 1, mitochondrial
Treponema pallidum TP0576   peptide chain release factor 2 (prfB)
Theileria parva TP04_0242   peptide chain release factor 2, putative
Wolbachia endosymbiont of Brugia malayi Wbm0295   protein chain release factor B

Essentiality

TP0576 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu3158 Mycobacterium tuberculosis essential nmpdr
b2891 Escherichia coli essential goodall
PBANKA_0802600 Plasmodium berghei Slow plasmo
Show/Hide essentiality data references
  • 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
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • 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
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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 TP0576 (Treponema pallidum), peptide chain release factor 2 (prfB)
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