Detailed view for LmjF.36.0870

Basic information

TDR Targets ID: 29453
Leishmania major, DEAH-box RNA helicase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.845 | Length (AA): 942 | MW (Da): 103788 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | 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

PF00270   DEAD/DEAH box helicase
PF00271   Helicase conserved C-terminal domain
PF04408   Helicase associated domain (HA2)

Gene Ontology

Mouse over links to read term descriptions.
GO:0005524   ATP binding  
GO:0004386   helicase activity  
GO:0003676   nucleic acid binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 9 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
202 589 1s2m (A) 48 407 17.00 0 1 0.53 -0.04
223 404 1wrb (A) 203 400 17.00 0 0.34 0.34 -0.34
2 138 4uos (A) 15 151 8.00 0.44 0 0.268935 -0.66
2 80 3v6i (B) 30 109 27.00 0.15 0.02 0.343364 -0.2
25 663 3o8b (A) 11 569 15.00 0 0.87 0.568144 1.32
91 941 2xau (A) 7 745 37.00 0 1 1.1532 -0.05
179 404 3llm (A) 374 563 37.00 0 1 0.558715 -0.74
190 938 5d0u (A) 93 748 41.00 0 1 1.10452 -0.04
425 543 2hjv (A) 224 333 15.00 0.04 0.94 0.361827 -0.94

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
Mid 40-60% percentile amastigotes, metacyclic. Fernandes MC
Show/Hide expression data references
  • Fernandes MC Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures.

Orthologs

Ortholog group members (OG5_153744)

Species Accession Gene Product
Leishmania braziliensis LbrM.35.0990   DEAH-box RNA helicase, putative
Leishmania donovani LdBPK_360930.1   pre-mRNA splicing factor ATP-dependent RNA helicase, putative
Leishmania infantum LinJ.36.0930   DEAH-box RNA helicase, putative
Leishmania major LmjF.36.0870   DEAH-box RNA helicase, putative
Leishmania mexicana LmxM.36.0870   DEAH-box RNA helicase, putative
Trypanosoma brucei gambiense Tbg972.10.6440   pre-mRNA splicing factor ATP-dependent RNA helicase, putative,DEAH-box RNA helicase, putative
Trypanosoma brucei Tb11.v5.0248   pre-mRNA splicing factor ATP-dependent RNA helicase, putative
Trypanosoma cruzi TcCLB.506679.50   pre-mRNA splicing factor ATP-dependent RNA helicase, putative

Essentiality

LmjF.36.0870 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.5280 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.5280 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.5280 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.5280 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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 LmjF.36.0870 (Leishmania major), DEAH-box RNA helicase, putative
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