Detailed view for LmjF.34.2620

Basic information

TDR Targets ID: 28386
Leishmania major, RNA helicase, putative,mitochondrial, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.3213 | Length (AA): 655 | MW (Da): 72845 | Paralog Number: 0

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

Druggability Group : DG2

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

PF00271   Helicase conserved C-terminal domain
PF12513   Mitochondrial degradasome RNA helicase subunit C terminal

Gene Ontology

Mouse over links to read term descriptions.
GO:0016817   hydrolase activity, acting on acid anhydrides  
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 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
75 248 1q0u (A) 6 211 21.00 0.0000000091 0.9 0.44 -0.7
77 451 1hv8 (A) 10 365 13.00 0 0.99 0.52 0.47
4 644 3rc3 (A) 89 662 21.00 0 1 1.01713 0.88
96 631 3rc3 (A) 188 649 40.00 0 1 1.05672 0.34

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_128486)

Species Accession Gene Product
Arabidopsis thaliana AT5G39840   putative ATP-dependent RNA helicase
Arabidopsis thaliana AT4G14790   ATP-dependent RNA helicase
Babesia bovis BBOV_IV011410   ATP-dependent RNA helicase, putative
Brugia malayi Bm1_18110   Helicase conserved C-terminal domain containing protein
Candida albicans CaO19.11994   similar to putative RNA helicase
Candida albicans CaO19.4519   similar to putative RNA helicase
Caenorhabditis elegans CELE_C08F8.2   Protein C08F8.2, isoform C
Dictyostelium discoideum DDB_G0278937   hypothetical protein
Drosophila melanogaster Dmel_CG9791   CG9791 gene product from transcript CG9791-RC
Homo sapiens ENSG00000156502   suppressor of var1, 3-like 1 (S. cerevisiae)
Leishmania braziliensis LbrM.20.2180   RNA helicase, putative,mitochondrial, putative
Leishmania donovani LdBPK_342450.1   ATP-dependent RNA and DNA helicase, mitochondrial, putative
Leishmania infantum LinJ.34.2450   RNA helicase, putative,mitochondrial, putative
Leishmania major LmjF.34.2620   RNA helicase, putative,mitochondrial, putative
Leishmania mexicana LmxM.33.2620   RNA helicase, putative,mitochondrial, putative
Loa Loa (eye worm) LOAG_02037   hypothetical protein
Mus musculus ENSMUSG00000020079   suppressor of var1, 3-like 1 (S. cerevisiae)
Neospora caninum NCLIV_032500   hypothetical protein
Oryza sativa 4336047   Os04g0459800
Oryza sativa 4334089   Os03g0746500
Plasmodium berghei PBANKA_1122600   ATP-dependent RNA helicase SUV3, putative
Plasmodium falciparum PF3D7_0623700   ATP-dependent RNA helicase SUV3, putative
Plasmodium knowlesi PKNH_1126500   ATP-dependent RNA helicase SUV3, putative
Plasmodium vivax PVX_114300   ATP-dependent DEAD box helicase, putative
Plasmodium yoelii PY04199   Helicase conserved C-terminal domain, putative
Saccharomyces cerevisiae YPL029W   Suv3p
Trypanosoma brucei gambiense Tbg972.4.1910   RNA helicase, putative,mitochondrial, putative
Trypanosoma brucei Tb927.4.1990   ATP-dependent RNA and DNA helicase, mitochondrial, putative
Trypanosoma congolense TcIL3000_4_1730   ATP-dependent RNA and DNA helicase, mitochondrial, putative
Trypanosoma cruzi TcCLB.510877.70   ATP-dependent RNA and DNA helicase, mitochondrial, putative
Toxoplasma gondii TGME49_232530   hypothetical protein
Theileria parva TP01_1165   ATP-dependent DEAD box helicase, putative

Essentiality

LmjF.34.2620 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.1990 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.1990 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.4.1990 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.4.1990 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C08F8.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_C08F8.2 Caenorhabditis elegans larval arrest wormbase
CELE_C08F8.2 Caenorhabditis elegans slow growth wormbase
PBANKA_1122600 Plasmodium berghei Essential plasmo
TGME49_232530 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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
  • 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.
  • 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.
  • 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.
  • 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

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
Species Known druggable target Linked compounds Reference
Homo sapiens suppressor of var1, 3-like 1 (S. cerevisiae) Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0051 1 1
0.0055 1 1
0.0057 0.5121 0.5
0.0057 1 0.5
0.0053 1 1
0.0054 1 1
0.0053 1 1
0.0056 0.7467 0
0.0053 1 0.5
0.0055 1 1

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.34.2620 (Leishmania major), RNA helicase, putative,mitochondrial, putative
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