Detailed view for Rv3401

Basic information

TDR Targets ID: 9108
Mycobacterium tuberculosis, Conserved protein
Source Database / ID:  Tuberculist 

pI: 5.6282 | Length (AA): 786 | MW (Da): 87316 | Paralog Number: 0

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

PF03632   Glycosyl hydrolase family 65 central catalytic domain
PF03633   Glycosyl hydrolase family 65, C-terminal domain
PF03636   Glycosyl hydrolase family 65, N-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0030246   carbohydrate binding  
GO:0003824   catalytic activity  
GO:0005975   carbohydrate metabolic process  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 4 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
2 763 4ktp (A) 4 765 23.00 0 1 1.18907 -0.07
7 749 1h54 (A) 5 749 28.00 0 1 1.27989 -0.16
7 750 1h54 (A) 5 741 30.00 0 1 1.26856 0.02
10 750 3wir (A) 6 756 28.00 0 1 1.24935 -0.28

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_129495)

Species Accession Gene Product
Candida albicans CaO19.13595   Vacuolar acid trehalase (alpha, alpha-trehalase)
Candida albicans CaO19.6214   Vacuolar acid trehalase (alpha, alpha-trehalase)
Dictyostelium discoideum DDB_G0287109   acid trehalase-like protein 1
Drosophila melanogaster Dmel_CG16965   CG16965 gene product from transcript CG16965-RC
Escherichia coli b1316   putative family 65 glycosyl hydrolase
Homo sapiens ENSG00000142102   ATH1, acid trehalase-like 1 (yeast)
Leishmania braziliensis LbrM.35.5490   glycosyl hydrolase, putative
Leishmania donovani LdBPK_365470.1   glycosyl hydrolase, putative
Leishmania infantum LinJ.36.5470   glycosyl hydrolase, putative
Leishmania major LmjF.36.5240   glycosyl hydrolase, putative
Leishmania mexicana LmxM.36.5240   glycosyl hydrolase, putative
Mycobacterium leprae ML0392c   Possible hydrolase
Mus musculus ENSMUSG00000062031   ATH1, acid trehalase-like 1 (yeast)
Mycobacterium tuberculosis Rv3401   Conserved protein
Mycobacterium ulcerans MUL_0906   glycosyl hydrolase
Saccharomyces cerevisiae YPR026W   alpha,alpha-trehalase ATH1
Schmidtea mediterranea mk4.006624.00  
Schmidtea mediterranea mk4.000843.07   Acid trehalase-like protein 1
Trypanosoma brucei gambiense Tbg972.11.11970   glycosyl hydrolase, putative
Trypanosoma brucei Tb927.11.10670   glycosyl hydrolase, putative
Trypanosoma congolense TcIL3000.11.11340   glycosyl hydrolase, putative
Trypanosoma cruzi TcCLB.506155.120   glycosyl hydrolase, putative

Essentiality

Rv3401 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3462 this record Mycobacterium tuberculosis non-essential nmpdr
Tb11.01.2440 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.2440 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.2440 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.01.2440 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b1316 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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

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
Saccharomyces cerevisiae alpha,alpha-trehalase ATH1 Compounds References
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 Rv3401 (Mycobacterium tuberculosis), Conserved protein
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