Detailed view for Rv0484c

Basic information

TDR Targets ID: 7394
Mycobacterium tuberculosis, Probable short-chain type oxidoreductase
Source Database / ID:  Tuberculist 

pI: 8.5916 | Length (AA): 251 | MW (Da): 26416 | 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
6 239 2jah (A) 5 246 41.00 0 1 1.33487 -0.79
6 248 3rku (A) 11 267 37.00 0 1 1.28773 -0.36
8 239 3p19 (A) 2 237 35.00 0 1 1.3729 -0.61
8 137 5o98 (A) 8 168 43.00 0.000000012 1 0.836528 0.29
8 201 4jig (A) 7 231 39.00 0 1 1.15151 0.09

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 60-80% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Dormant phase. 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_127267)

Species Accession Gene Product
Brugia malayi Bm1_41060   oxidoreductase
Candida albicans CaO19.4633   similar to insect-type short-chain alcohol dehydrogenase
Candida albicans CaO19.12103   similar to insect-type short-chain alcohol dehydrogenase
Dictyostelium discoideum DDB_G0282357   3-oxoacyl-[acyl-carrier protein] reductase
Drosophila melanogaster Dmel_CG3301   CG3301 gene product from transcript CG3301-RB
Drosophila melanogaster Dmel_CG40486   CG40486 gene product from transcript CG40486-RC
Drosophila melanogaster Dmel_CG9360   CG9360 gene product from transcript CG9360-RA
Drosophila melanogaster Dmel_CG40485   CG40485 gene product from transcript CG40485-RB
Drosophila melanogaster Dmel_CG1386   CG1386 gene product from transcript CG1386-RA
Escherichia coli b1539   NADP-dependent 3-hydroxy acid dehydrogenase
Echinococcus granulosus EgrG_000754200   oxidoreductase
Echinococcus multilocularis EmuJ_000754200   oxidoreductase
Homo sapiens ENSG00000278535   dehydrogenase/reductase (SDR family) member 11
Loa Loa (eye worm) LOAG_08687   oxidoreductase
Mus musculus ENSMUSG00000034449   dehydrogenase/reductase (SDR family) member 11
Mycobacterium tuberculosis Rv0484c   Probable short-chain type oxidoreductase
Mycobacterium ulcerans MUL_0028   short-chain dehydrogenase
Mycobacterium ulcerans MUL_4554   short-chain type oxidoreductase
Saccharomyces cerevisiae YMR226C   oxidoreductase
Schmidtea mediterranea mk4.005957.00   Dehydrogenase/reductase SDR family member 11
Schmidtea mediterranea mk4.000223.14   Dehydrogenase/reductase SDR family member 11
Schmidtea mediterranea mk4.002331.09  
Schmidtea mediterranea mk4.054278.00   Dehydrogenase/reductase SDR family member 11
Schmidtea mediterranea mk4.004675.05  
Trichomonas vaginalis TVAG_446780   short-chain dehydrogenase, putative

Essentiality

Rv0484c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu489 this record Mycobacterium tuberculosis non-essential nmpdr
b1539 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170

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 34.3% 143 aa Compounds References
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0106 1 1
0.0402 1 1
0.0046 0.3082 0.5
0.0068 0.2585 0.5
0.0106 0.2872 0.4772
0.0004 0.5 0.5
0.0088 0.6544 0.5
0.0131 0.5 0.5
0.0097 1 1
0.0113 1 1
0.016 0.577 1
0.0019 0.4322 0.5
0.0408 0.5144 0.5
0.0171 0.4063 0.5
0.0162 1 0.5
0.0009 0.5 0.5
0.004 0.5 0.5
0.0004 0.5 0.5
0.0045 1 0.5
0.0009 0.5 0.5
0.0066 0.3586 0.5
0.0058 1 1
0.0012 0.5 0.5
0.0053 1 1
0.008 0.5 0.5
0.0123 0.5 0.5
0.0009 0.5 0.5
0.0005 0.5 0.5
0.007 0.2916 1
0.007 0.2916 1
0.0016 0.5 0.5
0.0009 1 0.5
0.0071 0.3141 0
0.0132 0.3658 0.376
0.0021 0.3321 0.5
0.0085 1 0.5
0.0009 0.5 0.5
0.007 1 0.5
0.0012 0.5 0.5
0.0056 1 0.5
0.0082 1 0.5
0.0165 1 0.5
0.0004 0.5 0.5
0.0076 1 0.5
0.0009 0.5 0.5
0.016 0.577 1
0.0073 0.2873 0.3563
0.0073 0.4546 1
0.0106 0.5 0.5
0.0088 1 0.5
0.0013 0.5 0.5
0.0108 0.5 0.5
0.0114 1 0.5
0.007 1 0.5
0.0097 0.4304 0.5
0.0067 0.3468 0.5
0.0064 0.3508 0.5
0.0073 0.3811 1
0.0102 0.7451 0.5
0.0118 1 0.5
0.0005 0.5 0.5
0.0035 1 0.5
0.0408 0.5144 0.5
0.0408 0.5144 0.5
0.0119 0.2746 0
0.0089 0.5 0.5
0.0084 0.4283 1
0.0021 0.5 0.5
0.0068 1 0.5
0.0009 0.5 0.5
0.0218 0.5 0.5
0.0056 0.875 1
0.0004 0.5 0.5
0.0004 0.5 0.5
0.0009 0.5 0.5
0.0026 0.5 0.5
0.007 1 0.5
0.0068 1 0.5
0.0196 0.8679 0.5
0.0089 0.5 0.5
0.0009 0.5 0.5
0.0073 0.3811 1
0.0171 0.4063 0.5
0.0027 0.5 0.5
0.0013 1 0.5
0.0032 1 1
0.0057 0.284 0.6413
0.0093 0.5 0.5
0.0021 0.3321 0.5
0.011 0.3568 0.3299
0.0196 0.8679 0.5
0.0053 1 0.5
0.0009 0.7374 0.5
0.0039 1 0.5
0.0058 0.3931 1
0.0073 0.3141 0.4101
0.0114 1 0.5
0.0004 0.5 0.5
0.0157 0.5 0.5
0.007 0.2916 1
0.0196 0.8679 0.5
0.0087 0.5 0.5
0.0027 0.5 0.5
0.0106 1 0.5
0.0222 0.5 0.5
0.0004 0.5 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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Gene identifier Rv0484c (Mycobacterium tuberculosis), Probable short-chain type oxidoreductase
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