Detailed view for Rv2531c

Basic information

TDR Targets ID: 8592
Mycobacterium tuberculosis, Probable amino acid decarboxylase
Source Database / ID:  Tuberculist 

pI: 5.5121 | Length (AA): 947 | MW (Da): 106029 | Paralog Number: 0

Signal peptide: Y | 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

PF01276   Orn/Lys/Arg decarboxylase, major domain
PF03711   Orn/Lys/Arg decarboxylase, C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0030170   pyridoxal phosphate binding  
GO:0003824   catalytic activity  

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
4 127 4pfm (A) 108 236 31.00 0.34 0.41 0.28264 0.4
136 901 2vyc (A) 1 748 22.00 0 1 0.90127 0.56
336 561 1svv (A) 34 251 10.00 0.17 0.05 0.246048 0.46
377 500 3op7 (A) 86 199 32.00 0.1 0.58 0.21364 0.66

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_130799)

Species Accession Gene Product
Escherichia coli b0186   lysine decarboxylase 2, constitutive
Escherichia coli b4131   lysine decarboxylase, acid-inducible
Escherichia coli b4117   arginine decarboxylase
Entamoeba histolytica EHI_098380   Orn/Arg/Lys decarboxylase, putative
Mycobacterium leprae ML0524   Probable amino acid decarboxylase
Mycobacterium tuberculosis Rv2531c   Probable amino acid decarboxylase
Neospora caninum NCLIV_019490   lysine decarboxylase, putative
Oryza sativa 4334778   Os03g0848100
Plasmodium berghei PBANKA_1003400   lysine decarboxylase, putative
Plasmodium falciparum PF3D7_0405700   lysine decarboxylase, putative
Plasmodium knowlesi PKNH_0303800   lysine decarboxylase, putative
Plasmodium vivax PVX_000955   lysine decarboxylase, putative
Plasmodium yoelii PY00349   adi-related
Plasmodium yoelii PY01667   ERYTHROCYTE MEMBRANE PROTEIN PFEMP3
Schmidtea mediterranea mk4.046520.00  
Toxoplasma gondii TGME49_280700   arginine decarboxylase

Essentiality

Rv2531c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2575 this record Mycobacterium tuberculosis non-essential nmpdr
b0186 Escherichia coli non-essential goodall
b4117 Escherichia coli non-essential goodall
b4131 Escherichia coli non-essential goodall
TGME49_280700 Toxoplasma gondii Essentiality uncertain sidik
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.
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • 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.

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

32 literature references were collected for this gene.

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 Rv2531c (Mycobacterium tuberculosis), Probable amino acid decarboxylase
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