Detailed view for Rv1701

Basic information

TDR Targets ID: 8081
Mycobacterium tuberculosis, Probable integrase/recombinase
Source Database / ID:  Tuberculist 

pI: 10.7727 | Length (AA): 311 | MW (Da): 33517 | Paralog Number: 1

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

PF00589   Phage integrase family
PF02899   Phage integrase, N-terminal SAM-like domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0009009   site-specific recombinase activity  
GO:0003677   DNA binding  
GO:0007059   chromosome segregation  
GO:0007049   cell cycle  
GO:0006310   DNA recombination  
GO:0051301   cell division  
GO:0015074   DNA integration  

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
3 111 3nrw (A) 8 107 20.00 0 1 0.622582 -0.8
6 309 5hxy (A) 7 282 32.00 0 1 1.26379 0.27
7 302 1a0p (A) 7 290 45.00 0 1 1.39377 -0.17

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
Lower 20-40% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Dormant phase. 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_129974)

Species Accession Gene Product
Chlamydia trachomatis CT_864   tyrosine recombinase XerD
Chlamydia trachomatis CT_347   tyrosine recombinase XerC
Escherichia coli b2894   site-specific tyrosine recombinase
Mycobacterium leprae ML1365   PROBABLE INTEGRASE/RECOMBINASE
Mycobacterium leprae ML1600c   PROBABLE INTEGRASE/RECOMBINASE XERC
Mycobacterium tuberculosis Rv1701   Probable integrase/recombinase
Mycobacterium tuberculosis Rv2894c   Probable integrase/recombinase XerC
Mycobacterium ulcerans MUL_2065   site-specific tyrosine recombinase XerC
Mycobacterium ulcerans MUP058c   site-specific recombinase
Mycobacterium ulcerans MUL_1690   site-specific tyrosine recombinase XerD
Treponema pallidum TP0391   integrase/recombinase (codV)
Treponema pallidum TP0395   integrase/recombinase (xprB)
Wolbachia endosymbiont of Brugia malayi Wbm0732   site-specific recombinase XerD

Essentiality

Rv1701 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1730 this record Mycobacterium tuberculosis essential nmpdr
b2894 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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
  • 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

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

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 Rv1701 (Mycobacterium tuberculosis), Probable integrase/recombinase
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