Detailed view for Rv2879c

Basic information

TDR Targets ID: 8824
Mycobacterium tuberculosis, Conserved hypothetical protein
Source Database / ID:  Tuberculist 

pI: 10.8535 | Length (AA): 189 | MW (Da): 20413 | Paralog Number: 1

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

PF04055   Radical SAM superfamily

Gene Ontology

Mouse over links to read term descriptions.
GO:0005737   cytoplasm  
GO:0051536   iron-sulfur cluster binding  
GO:0008173   RNA methyltransferase activity  
GO:0003824   catalytic activity  
GO:0006364   rRNA processing  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
1 187 3rfa (B) 178 361 41.00 0 1 1.48522 -0.59

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
Mid 40-60% percentile Dormant phase. murphy
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_128806)

Species Accession Gene Product
Arabidopsis thaliana AT2G39670   radical SAM domain-containing protein
Arabidopsis thaliana AT3G19630   radical SAM domain-containing protein
Arabidopsis thaliana AT1G60230   radical SAM domain-containing protein
Babesia bovis BBOV_III008940   radical SAM domain containing protein
Cryptosporidium hominis Chro.40137   hypothetical protein
Cryptosporidium parvum cgd4_1160   conserved protein with transmembrane region at C-terminus
Dictyostelium discoideum DDB_G0288255   hypothetical protein
Escherichia coli b2517   dual specificity 23S rRNA m(2)A2503, tRNA m(2)A37 methyltransferase, SAM-dependent
Mycobacterium tuberculosis Rv2879c   Conserved hypothetical protein
Mycobacterium tuberculosis Rv2880c   Conserved hypothetical protein
Mycobacterium ulcerans MUL_2078   ribosomal RNA large subunit methyltransferase N
Neospora caninum NCLIV_004040   Radical SAM enzyme, Cfr family, related
Neospora caninum NCLIV_007530   UvrD-like DNA helicase, C terminal, related
Neospora caninum NCLIV_022230   hypothetical protein
Oryza sativa 4326401   Os01g0973400
Oryza sativa 4331979   Os03g0202300
Oryza sativa 4326553   Os01g0640800
Plasmodium berghei PBANKA_1035300   radical SAM protein, putative
Plasmodium falciparum PF3D7_1406900   radical SAM protein, putative
Plasmodium knowlesi PKNH_1351200   radical SAM protein, putative
Plasmodium vivax PVX_086085   Fe-S-cluster redox enzyme, putative
Plasmodium yoelii PY01072   unnamed protein product
Toxoplasma gondii TGME49_209790   radical SAM domain-containing protein
Toxoplasma gondii TGME49_252465   radical SAM domain-containing protein
Treponema pallidum TP0068   hypothetical protein
Theileria parva TP04_0797   hypothetical protein, conserved

Essentiality

Rv2879c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2926 this record Mycobacterium tuberculosis non-essential nmpdr
mtu2927 Mycobacterium tuberculosis non-essential nmpdr
b2517 Escherichia coli non-essential goodall
PBANKA_1035300 Plasmodium berghei Essential plasmo
TGME49_252465 Toxoplasma gondii Essentiality uncertain sidik
TGME49_209790 Toxoplasma gondii Essentiality uncertain sidik
TGME49_252465 Toxoplasma gondii Probably essential sidik
TGME49_209790 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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.
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
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 Rv2879c (Mycobacterium tuberculosis), Conserved hypothetical protein
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