Detailed view for Rv1964

Basic information

TDR Targets ID: 10056
Mycobacterium tuberculosis, Conserved hypothetical integral membrane protein YrbE3A
Source Database / ID:  Tuberculist 

pI: 7.0389 | Length (AA): 265 | MW (Da): 27494 | Paralog Number: 4

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 5

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

PF02405   Permease MlaE

Gene Ontology

Mouse over links to read term descriptions.
GO:0043190   ATP-binding cassette (ABC) transporter complex  
GO:0006810   transport  

Metabolic Pathways

ABC transporters (KEGG)

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
76 169 4mow (C) 116 238 35.00 0.8 0.18 0.296417 1.49

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
Upper 80-100% percentile Dormant phase. murphy
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Dormant phase. hasan
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_130961)

Species Accession Gene Product
Arabidopsis thaliana AT1G19800   trigalactosyldiacylglycerol 1
Escherichia coli b3194   ABC transporter maintaining OM lipid asymmetry, inner membrane permease protein
Mycobacterium leprae ML2587   CONSERVED HYPOTHETICAL INTEGRAL MEMBRANE PROTEIN YRBE1A
Mycobacterium tuberculosis Rv0587   Conserved hypothetical integral membrane protein YrbE2A
Mycobacterium tuberculosis Rv0588   Conserved hypothetical integral membrane protein YrbE2B
Mycobacterium tuberculosis Rv1964   Conserved hypothetical integral membrane protein YrbE3A
Mycobacterium tuberculosis Rv3501c   Conserved integral membrane protein YrbE4A. Possible ABC transporter.
Mycobacterium tuberculosis Rv0167   Conserved integral membrane protein YrbE1A
Mycobacterium ulcerans MUL_2872   integral membrane protein YrbE3A
Mycobacterium ulcerans MUL_4921   integral membrane protein YrbE6A
Mycobacterium ulcerans MUL_1060   integral membrane protein YrbE1A
Mycobacterium ulcerans MUL_3916   integral membrane protein YrbE3A
Mycobacterium ulcerans MUL_3794   YrbE family protein, YrbE5A
Mycobacterium ulcerans MUL_4064   membrane protein YrbE4A
Oryza sativa 4336607   Os04g0553000
Wolbachia endosymbiont of Brugia malayi Wbm0617   ABC-type transport system involved in resistance to organic solvents, permease component

Essentiality

Rv1964 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu595 Mycobacterium tuberculosis non-essential nmpdr
mtu596 Mycobacterium tuberculosis essential nmpdr
b3194 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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.
  • 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.

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.

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User comments

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Gene identifier Rv1964 (Mycobacterium tuberculosis), Conserved hypothetical integral membrane protein YrbE3A
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