Detailed view for Rv2889c

Basic information

TDR Targets ID: 9999
Mycobacterium tuberculosis, Probable elongation factor Tsf (EF-ts)
Source Database / ID:  Tuberculist 

pI: 5.0103 | Length (AA): 271 | MW (Da): 28755 | 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

PF00889   Elongation factor TS

Gene Ontology

Mouse over links to read term descriptions.
GO:0005622   intracellular  
GO:0005515   protein binding  
GO:0003746   translation elongation factor activity  
GO:0006414   translational elongation  

Metabolic Pathways

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

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
2 271 3avx (A) 2 264 40.00 0 1 1.38561 0.42
6 269 1aip (C) 4 195 42.00 0 1 0.76447 1.91
141 269 1tfe (A) 57 195 41.00 0 1 0.858515 -0.38

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 20-40% percentile Dormant phase. murphy
Upregulation Percent Ranking Stage Dataset
Lower 0-20% 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_127934)

Species Accession Gene Product
Arabidopsis thaliana AT4G11120   putative translation elongation factor Ts
Babesia bovis BBOV_II003360   elongation factor TS, putative
Babesia bovis BBOV_III009630   conserved hypothetical protein
Brugia malayi Bm1_50845   Elongation factor TS family protein
Caenorhabditis elegans CELE_F55C5.5   Protein TSFM-1
Chlamydia trachomatis CT_679   elongation factor TS
Dictyostelium discoideum DDB_G0286399   elongation factor Ts
Drosophila melanogaster Dmel_CG6412   CG6412 gene product from transcript CG6412-RA
Escherichia coli b0170   translation elongation factor EF-Ts
Echinococcus granulosus EgrG_000126100   elongation factor Ts
Echinococcus multilocularis EmuJ_000126100   elongation factor Ts
Homo sapiens ENSG00000123297   Ts translation elongation factor, mitochondrial
Leishmania braziliensis LbrM.29.0730   hypothetical protein, conserved
Leishmania donovani LdBPK_290750.1   Elongation factor Ts, mitochondrial, putative
Leishmania infantum LinJ.29.0750   hypothetical protein, conserved
Leishmania major LmjF.29.0720   hypothetical protein, conserved
Leishmania mexicana LmxM.08_29.0720   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_04276   elongation factor TS family protein
Mycobacterium leprae ML1597c   PROBABLE ELONGATION FACTOR TSF (EF-TS)
Mus musculus ensembl-mmu:ENSMUSG00000040521   Ts translation elongation factor, mitochondrial
Mycobacterium tuberculosis Rv2889c   Probable elongation factor Tsf (EF-ts)
Mycobacterium ulcerans MUL_2068   elongation factor Ts
Neospora caninum NCLIV_003420   elongation factor ts, putative
Oryza sativa 4345504   Os08g0399600
Plasmodium berghei PBANKA_0403500   elongation factor (EF-TS), putative
Plasmodium falciparum PF3D7_0305000   elongation factor Ts
Plasmodium knowlesi PKNH_0838100   elongation factor (EF-TS), putative
Plasmodium vivax PVX_119375   elongation factor (EF-TS), putative
Plasmodium yoelii PY07445   translation elongation factor Ts
Schistosoma mansoni Smp_148540   elongation factor ts
Schmidtea mediterranea mk4.000194.04   Elongation factor Ts, mitochondrial
Trypanosoma brucei gambiense Tbg972.3.3920   elongation factor ts, putative
Trypanosoma brucei Tb927.3.3630   Elongation factor Ts, mitochondrial, putative
Trypanosoma congolense TcIL3000_3_2320   Elongation factor Ts, mitochondrial, putative
Trypanosoma cruzi TcCLB.506989.140   Elongation factor Ts, mitochondrial, putative
Trypanosoma cruzi TcCLB.503811.60   Elongation factor Ts, mitochondrial, putative
Toxoplasma gondii TGME49_209010   elongation factor TS protein
Treponema pallidum TP0605   elongation factor Ts
Theileria parva TP04_0253   hypothetical protein
Wolbachia endosymbiont of Brugia malayi Wbm0807   elongation factor Ts

Essentiality

Rv2889c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2936 this record Mycobacterium tuberculosis essential nmpdr
Tb927.3.3630 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.3.3630 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.3.3630 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.3.3630 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b0170 Escherichia coli essential goodall
CELE_F55C5.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_F55C5.5 Caenorhabditis elegans larval arrest wormbase
CELE_F55C5.5 Caenorhabditis elegans slow growth wormbase
PBANKA_0403500 Plasmodium berghei Essential plasmo
TGME49_209010 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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

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): 0.2

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.

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User comments

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Gene identifier Rv2889c (Mycobacterium tuberculosis), Probable elongation factor Tsf (EF-ts)
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