Detailed view for Rv1895

Basic information

TDR Targets ID: 8208
Mycobacterium tuberculosis, Possible dehydrogenase

Source Database / ID:  Tuberculist 

pI: 4.584 | Length (AA): 384 | MW (Da): 39479 | 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

PF00107   Zinc-binding dehydrogenase
PF08240   Alcohol dehydrogenase GroES-like domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0016491   oxidoreductase activity  
GO:0008270   zinc ion binding  
GO:0005488   binding  
GO:0003824   catalytic activity  
GO:0055114   oxidation reduction  
GO:0008152   metabolic process  

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
1 339 4cpd (A) 1 343 38.00 0 1 1.37031 -0.43
10 361 3krt (A) 56 445 21.00 0 1 1.00217 0.29
169 247 4izh (A) 170 256 34.00 0.61 1 0.666129 -0.53

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. hasan
Upregulation Percent Ranking Stage Dataset
Upper 60-80% 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_128603)

Species Accession Gene Product
Candida albicans CaO19.4287   similar to several Bacterial Zinc-binding Dehydrogenases and to S. cerevisiae XYL2 (YLR070C) xylitol dehydrogenase
Candida albicans CaO19.11763   similar to several Bacterial Zinc-binding Dehydrogenases and to S. cerevisiae XYL2 (YLR070C) xylitol dehydrogenase
Escherichia coli b0608   putative Zn-dependent NAD(P)-binding oxidoreductase
Entamoeba histolytica EHI_042260   NADP-dependent alcohol dehydrogenase, putative
Mycobacterium tuberculosis Rv1895   Possible dehydrogenase
Mycobacterium ulcerans MUL_2962   dehydrogenase
Trichomonas vaginalis TVAG_228780   alcohol dehydrogenase, putative
Trichomonas vaginalis TVAG_454470   alcohol dehydrogenase, putative
Trichomonas vaginalis TVAG_344880   alcohol dehydrogenase, putative

Essentiality

Rv1895 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1926 this record Mycobacterium tuberculosis non-essential nmpdr
b0608 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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

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): 0.3


Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Pseudomonas putida Glutathione-independent formaldehyde dehydrogenase Compounds References
By sequence similarity to non orthologous druggable targets
Species Target Length Identity Alignment span Linked Drugs Reference
Rhodobacter capsulatus 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A dehydrogenase 314 aa 24.0% 313 aa Compounds References
Rattus norvegicus Sorbitol dehydrogenase 357 aa 28.4% 359 aa Compounds References
Equus caballus Alcohol dehydrogenase 374 aa 26.0% 350 aa Compounds References

Obtained from network model

Ranking Plot


Putative Drugs List


Compound Raw Global Species
0.0581 0.2856 0.3609
0.0571 0.4361 0.5903
0.0155 0.3957 0.5326
0.0571 0.4361 0.5903
0.0799 0.2936 0.3707
0.0155 0.5108 1
0.0571 0.4361 0.5903
0.0571 0.4361 0.5903
0.0574 0.2676 0.3369
0.0155 0.3865 0.5
0.0127 0.3158 0.4215
0.0522 0.4332 0.5894
0.0155 0.4087 0.5326
0.0571 0.4361 0.5903
0.0865 0.3728 0.4756
0.051 0.3433 0.4621
0.0296 0.3628 0.5813
0.051 0.28 0.4095
0.0821 0.3187 0.4594
0.0811 0.269 0.3373
0.0155 0.3007 0.5674
0.0584 0.2886 0.3623
0.0141 0.518 1
0.051 0.28 0.4095
0.0142 0.2707 0.4932
0.0799 0.2936 0.3707
0.0155 0.3957 0.5326
0.0551 0.4288 0.5851
0.0699 0.3011 0.439
0.0515 0.4316 0.5813
0.0515 0.4316 0.5813
0.0574 0.2676 0.3369
0.0811 0.269 0.3373
0.0149 0.2969 0.5931

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 Rv1895 (Mycobacterium tuberculosis), Possible dehydrogenase
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