Detailed view for TP0493

Basic information

TDR Targets ID: 596459
Treponema pallidum, RNA polymerase sigma factor RpoD
Source Database / ID:  KEGG  

pI: 7.7502 | Length (AA): 611 | MW (Da): 70902 | 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

PF00140   Sigma-70 factor, region 1.2
PF03979   Sigma-70 factor, region 1.1
PF04539   Sigma-70 region 3
PF04542   Sigma-70 region 2
PF04545   Sigma-70, region 4

Gene Ontology

Mouse over links to read term descriptions.
GO:0006355   regulation of transcription, DNA-dependent  
GO:0016987   sigma factor activity  
GO:0003700   transcription factor activity  
GO:0003677   DNA binding  
GO:0006352   transcription initiation  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
7 610 4lk1 (F) 6 612 37.00 0 1 1.18504 1.3
13 610 4lk1 (F) 12 612 41.00 0 1 1.22732 1.13
538 599 4g6d (A) 538 599 63.00 0.000000000012 1 1.01107 -1.88

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_130714)

Species Accession Gene Product
Arabidopsis thaliana AT1G08540   RNA polymerase sigma subunit 2
Chlamydia trachomatis CT_615   RNA polymerase sigma factor SigA
Escherichia coli b3067   RNA polymerase, sigma 70 (sigma D) factor
Mycobacterium leprae ML1022c   RNA polymerase sigma factor SigA
Mycobacterium tuberculosis Rv2703   RNA polymerase sigma factor SigA (sigma-A)
Mycobacterium ulcerans MUL_3341   RNA polymerase sigma factor
Oryza sativa 4350441   Os11g0448400
Oryza sativa 4332388   Os03g0271100
Schmidtea mediterranea mk4.046473.00  
Treponema pallidum TP0493   RNA polymerase sigma factor RpoD
Wolbachia endosymbiont of Brugia malayi Wbm0393   DNA-directed RNA polymerase sigma 70 subunit, RpoD

Essentiality

TP0493 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b3067 Escherichia coli essential goodall
Show/Hide essentiality data references
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.

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 TP0493 (Treponema pallidum), RNA polymerase sigma factor RpoD
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