Detailed view for Rv1613

Basic information

TDR Targets ID: 9986
Mycobacterium tuberculosis, Probable tryptophan synthase, alpha subunit TrpA

Source Database / ID:  Tuberculist 

pI: 4.6766 | Length (AA): 270 | MW (Da): 27728 | 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

PF00290   Tryptophan synthase alpha chain

Gene Ontology

Mouse over links to read term descriptions.
GO:0004834   tryptophan synthase activity  
GO:0003824   catalytic activity  
GO:0008152   metabolic process  
GO:0006568   tryptophan metabolic process  

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
8 267 5tch (A) 8 267 99.99 0 1 2.21206 -1.98

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:

  • 5OCW:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 5TCF:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 5TCG:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 5TCH:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 5TCI:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 5TCJ:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 6DU1:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 6DUA:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 6DWE:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 6E9P:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Dormant phase, Dormant phase. hasan murphy
Show/Hide expression data references
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.

Orthologs

Ortholog group members (OG5_130207)

Species Accession Gene Product
Arabidopsis thaliana AT4G02610   tryptophan synthase alpha chain
Arabidopsis thaliana AT3G54640   tryptophan synthase alpha chain
Chlamydia trachomatis CT_171   tryptophan synthase subunit alpha
Escherichia coli b1260   tryptophan synthase, alpha subunit
Mycobacterium leprae ML1273   Probable tryptophan synthase, alpha subunit TrpA
Mycobacterium tuberculosis Rv1613   Probable tryptophan synthase, alpha subunit TrpA
Mycobacterium ulcerans MUL_1593   tryptophan synthase subunit alpha
Oryza sativa 4334425   Os03g0797000
Oryza sativa 9268807   Os03g0797550
Oryza sativa 4334427   Os03g0797400
Oryza sativa 4342571   Os07g0182100
Schmidtea mediterranea mk4.075761.00  

Essentiality

Rv1613 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1641 this record Mycobacterium tuberculosis essential nmpdr
b1260 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • 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
  • 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

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): 0.2


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

1 literature reference was collected for this gene.

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 Rv1613 (Mycobacterium tuberculosis), Probable tryptophan synthase, alpha subunit TrpA
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