Detailed view for Rv2509

Basic information

TDR Targets ID: 8576
Mycobacterium tuberculosis, Probable short-chain type dehydrogenase/reductase

Source Database / ID:  Tuberculist 

pI: 8.8527 | Length (AA): 268 | MW (Da): 28013 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0

Druggability Group : DG2

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

PF00106   short chain dehydrogenase

Gene Ontology

Mouse over links to read term descriptions.
GO:0016491   oxidoreductase activity  
GO:0005488   binding  
GO:0003824   catalytic activity  
GO:0008152   metabolic process  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 5 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
8 197 1vl8 (A) 8 200 25.00 0 1 1.15916 -1.29
8 267 3t4x (A) 6 258 24.00 0 1 1.25435 -0.13
11 257 4bmv (A) 6 249 32.00 0 1 1.37484 -0.72
12 94 5l53 (A) 16 104 37.00 0.013 1 0.678201 -0.79
12 209 2ae2 (A) 12 203 27.00 0.00000000032 1 1.10831 -0.8

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 0-20% percentile Dormant phase, Dormant phase. hasan murphy
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_160488)

Species Accession Gene Product
Mycobacterium tuberculosis Rv2509   Probable short-chain type dehydrogenase/reductase
Mycobacterium ulcerans MUL_3788   short-chain type dehydrogenase/reductase
Oryza sativa 4340815   Os06g0298700
Oryza sativa 4340818   Os06g0299300
Oryza sativa 4334949   Os04g0116600
Oryza sativa 4340816   Os06g0299100
Oryza sativa 4340820   Os06g0300000
Oryza sativa 4340817   Os06g0299200

Essentiality

Rv2509 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2552 this record Mycobacterium tuberculosis non-essential nmpdr
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
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • 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.
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

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): 0.4


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
Species Target Length Identity Alignment span Linked Drugs Reference
Macaca mulatta Hydroxysteroid 11-beta dehydrogenase 1 140 aa 26.1% 142 aa Compounds References

Obtained from network model

Ranking Plot


Putative Drugs List


Compound Raw Global Species
0.0097 1 1
0.0089 0.5 0.5
0.0067 0.3468 0.5
0.0009 0.7374 0.5
0.0132 0.3658 0.376
0.0045 1 0.5
0.0093 0.5 0.5
0.0171 0.4063 0.5
0.0106 1 1
0.0073 0.3811 1
0.0066 0.3586 0.5
0.0068 1 0.5
0.011 0.3568 0.3299
0.0157 0.5 0.5
0.0131 0.5 0.5
0.0162 1 0.5
0.0021 0.3321 0.5
0.0053 1 0.5
0.0056 1 0.5
0.0087 0.5 0.5
0.0027 0.5 0.5
0.0068 1 0.5
0.007 1 0.5
0.0009 0.5 0.5
0.0064 0.3508 0.5
0.0171 0.4063 0.5
0.004 0.5 0.5
0.0402 1 1
0.0009 0.5 0.5
0.0032 1 1
0.0005 0.5 0.5
0.0021 0.3321 0.5
0.0035 1 0.5
0.0106 1 0.5
0.0046 0.3082 0.5
0.0102 0.7451 0.5
0.0076 1 0.5
0.0009 0.5 0.5
0.0009 0.5 0.5
0.0009 0.5 0.5
0.008 0.5 0.5
0.0108 0.5 0.5
0.0106 0.5 0.5
0.0016 0.5 0.5
0.007 1 0.5
0.0013 0.5 0.5
0.0073 0.4546 1
0.0053 1 1
0.0057 0.284 0.6413
0.0196 0.8679 0.5
0.0005 0.5 0.5
0.0106 0.2872 0.4772
0.0004 0.5 0.5
0.0056 0.875 1
0.0088 1 0.5
0.0004 0.5 0.5
0.0088 0.6544 0.5
0.0084 0.4283 1
0.0012 0.5 0.5
0.0021 0.5 0.5
0.0027 0.5 0.5
0.0013 1 0.5
0.0073 0.2873 0.3563
0.0009 0.5 0.5
0.0026 0.5 0.5
0.007 0.2916 1
0.0114 1 0.5
0.0058 0.3931 1
0.007 1 0.5
0.0073 0.3141 0.4101
0.0196 0.8679 0.5
0.0071 0.3141 0
0.0004 0.5 0.5
0.0114 1 0.5
0.0097 0.4304 0.5
0.016 0.577 1
0.0004 0.5 0.5
0.0009 0.5 0.5
0.007 0.2916 1
0.016 0.577 1
0.0408 0.5144 0.5
0.0118 1 0.5
0.0009 0.5 0.5
0.0004 0.5 0.5
0.0085 1 0.5
0.0408 0.5144 0.5
0.0004 0.5 0.5
0.0089 0.5 0.5
0.0019 0.4322 0.5
0.0012 0.5 0.5
0.007 0.2916 1
0.0068 0.2585 0.5
0.0222 0.5 0.5
0.0165 1 0.5
0.0408 0.5144 0.5
0.0004 0.5 0.5
0.0073 0.3811 1
0.0218 0.5 0.5
0.0123 0.5 0.5
0.0113 1 1
0.0119 0.2746 0
0.0058 1 1
0.0082 1 0.5
0.0196 0.8679 0.5
0.0039 1 0.5
0.0009 1 0.5

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 Rv2509 (Mycobacterium tuberculosis), Probable short-chain type dehydrogenase/reductase
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