Detailed view for Rv1464

Basic information

TDR Targets ID: 5781
Mycobacterium tuberculosis, Probable cysteine desulfurase Csd

Source Database / ID:  Tuberculist 

pI: 6.0438 | Length (AA): 417 | MW (Da): 44596 | 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

PF00266   Aminotransferase class-V

Gene Ontology

Mouse over links to read term descriptions.
GO:0031071   cysteine desulfurase activity  
GO:0030170   pyridoxal phosphate binding  
GO:0003824   catalytic activity  
GO:0008152   metabolic process  
GO:0006534   cysteine metabolic process  

Metabolic Pathways

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
6 414 4lw2 (A) 2 399 38.00 0 1 1.47432 -0.65
8 415 4w91 (A) 11 414 47.00 0 1 1.60392 -0.87
8 415 1jf9 (A) 3 406 46.00 0 1 1.57292 -0.76

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
Mid 40-60% percentile Dormant phase. hasan
Show/Hide expression data references
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.

Orthologs

Ortholog group members (OG5_128800)

Species Accession Gene Product
Arabidopsis thaliana AT1G08490   cysteine desulfurase 2
Babesia bovis BBOV_IV003350   cysteine desulfurase
Chlamydia trachomatis CT_687   cysteine desulfurase-like protein
Escherichia coli b2810   cysteine sulfinate desulfinase
Escherichia coli b1680   cysteine desulfurase, stimulated by SufE
Mycobacterium leprae ML0842   Probable cysteine desulfurase 1 Csd1
Mycobacterium leprae ML0596   Probable cysteine desulfurase Csd
Mycobacterium tuberculosis Rv1464   Probable cysteine desulfurase Csd
Mycobacterium ulcerans MUL_1865   cysteine desulfurase
Neospora caninum NCLIV_059990   selenocysteine lyase, putative
Oryza sativa 4351999   Os12g0287300
Plasmodium berghei PBANKA_0614300   cysteine desulfurase
Plasmodium falciparum PF3D7_0716600   cysteine desulfurase
Plasmodium knowlesi PKNH_0311200   cysteine desulfurase, putative
Plasmodium vivax PVX_000600   cysteine desulfurase, putative
Plasmodium yoelii PY06105   Arabidopsis thaliana T27G7.17, putative
Toxoplasma gondii TGME49_216170   SufS subfamily cysteine desulfurase
Treponema pallidum TP0614   nitrogen fixation protein (nifS-1)
Theileria parva TP01_1094   cysteine desulfurase, putative

Essentiality

Rv1464 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1487 this record Mycobacterium tuberculosis essential nmpdr
b1680 Escherichia coli non-essential goodall
b2810 Escherichia coli non-essential goodall
PBANKA_0614300 Plasmodium berghei Slow plasmo
TGME49_216170 Toxoplasma gondii Probably essential sidik
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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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

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.

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 Rv1464 (Mycobacterium tuberculosis), Probable cysteine desulfurase Csd
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