Detailed view for Tb927.11.11770

Basic information

TDR Targets ID: 14442
Trypanosoma brucei, Eukaryotic translation initiation factor 4E-3
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.4552 | Length (AA): 442 | MW (Da): 47963 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0

Druggability Group : DG3

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

PF01652   Eukaryotic initiation factor 4E

Gene Ontology

Mouse over links to read term descriptions.
GO:0005737   cytoplasm  
GO:0003743   translation initiation factor activity  
GO:0003723   RNA binding  
GO:0006413   translational initiation  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 5 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
7 50 1jvr (A) 91 134 20.00 0.14 0.03 0.328073 -0.54
233 413 2jgb (A) 49 217 30.00 0.0000000094 1 0.735931 -0.53
233 435 2jgb (A) 49 232 25.00 0 1 0.665617 -0.47
241 418 5abv (A) 72 236 27.00 0 1 0.779928 -1.19
245 414 3m94 (A) 56 214 27.00 0 1 0.754788 -1.03

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 Procyclic. Siegel TN
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Bloodstream Form. Siegel TN
Show/Hide expression data references
  • Siegel TN Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites.

Orthologs

Ortholog group members (OG5_143232)

Species Accession Gene Product
Brugia malayi Bm1_07620   eukaryotic translation initiation factor 4E-1
Caenorhabditis elegans CELE_F53A2.6   Protein IFE-1, isoform B
Leishmania braziliensis LbrM.28.2700   eukaryotic translation initiation factor, putative
Leishmania donovani LdBPK_282690.1   Eukaryotic translation initiation factor 4E-3
Leishmania infantum LinJ.28.2690   eukaryotic translation initiation factor, putative
Leishmania major LmjF.28.2500   eukaryotic translation initiation factor, putative
Leishmania mexicana LmxM.28.2500   eukaryotic translation initiation factor, putative
Loa Loa (eye worm) LOAG_06877   eukaryotic translation initiation factor 4E-1
Onchocerca volvulus OVOC2372   Putative eukaryotic translation initiation factor 4e
Trypanosoma brucei gambiense Tbg972.11.13210   eukaryotic translation initiation factor 4e, putative
Trypanosoma brucei Tb927.11.11770   Eukaryotic translation initiation factor 4E-3
Trypanosoma congolense TcIL3000.11.12420   Eukaryotic translation initiation factor 4E-3
Trypanosoma cruzi TcCLB.508827.30   Eukaryotic translation initiation factor 4E-3

Essentiality

Tb927.11.11770 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.3630 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.01.3630 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.3630 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.01.3630 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F53A2.6 Caenorhabditis elegans embryonic lethal wormbase
CELE_F53A2.6 Caenorhabditis elegans sterile wormbase
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • 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.

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) decreased (PATO:0000468) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: decreased cell proliferation (significant loss of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) decreased (PATO:0000468) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: decreased cell proliferation (significant loss of fitness) in differentiation of procyclic to bloodstream forms . References: 21363968

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): 0.3

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
Species Target Length Identity Alignment span Linked Drugs Reference
Oryctolagus cuniculus Eukaryotic translation initiation factor 4E 217 aa 24.7% 186 aa Compounds References
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

1 literature reference was collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier Tb927.11.11770 (Trypanosoma brucei), Eukaryotic translation initiation factor 4E-3
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