Detailed view for LmjF.36.3000

Basic information

TDR Targets ID: 21026
Leishmania major, ATP-dependent RNA helicase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.333 | Length (AA): 968 | MW (Da): 107972 | 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
PF08148   DSHCT (NUC185) domain
PF13234   rRNA-processing arch domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0003724   RNA helicase activity  
GO:0008026   ATP-dependent helicase activity  
GO:0005524   ATP binding  
GO:0004386   helicase activity  
GO:0003723   RNA binding  
GO:0003676   nucleic acid binding  
GO:0006401   RNA catabolic process  

Metabolic Pathways

RNA degradation (KEGG)

Structural information

Modbase 3D models:

There are 6 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
5 492 1fuu (B) 11 394 18.00 0 1 0.13 0.35
31 190 1q0u (A) 17 193 21.00 0.000000056 1 0.47 -1.55
3 968 4xgt (A) 142 1106 44.00 0 1 1.47493 -0.09
6 968 4u4c (A) 117 1073 47.00 0 1 1.55583 -0.73
41 197 3ber (A) 46 218 18.00 0 1 0.44659 -1.39
41 197 3fe2 (A) 116 292 21.00 0 1 0.45259 -1.45

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. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile 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_127259)

Species Accession Gene Product
Arabidopsis thaliana AT1G70070   DEAD-box ATP-dependent RNA helicase ISE2
Arabidopsis thaliana AT1G59760   putative RNA helicase MTR4
Arabidopsis thaliana AT2G06990   protein HUA ENHANCER 2
Babesia bovis BBOV_II005660   DSHCT (NUC185) domain containing DEAD/DEAH box helicase family protein
Brugia malayi Bm1_42300   symbol
Candida albicans CaO19.1335   DEAD-box helicase required for mRNA transport, rRNA processing
Candida albicans CaO19.8915   DEAD-box RNA helicase for mRNA export
Candida albicans CaO19_1335   hypothetical protein
Caenorhabditis elegans CELE_W08D2.7   Protein MTR-4
Cryptosporidium hominis Chro.80294   ATP-dependent RNA helicase; ATP-dependent RNA helicase
Cryptosporidium parvum cgd8_2520   Mtr4p like SKI family SFII helicase
Dictyostelium discoideum DDB_G0275633   DEAD/DEAH box helicase
Drosophila melanogaster Dmel_CG4152   lethal (2) 35Df
Echinococcus granulosus EgrG_000456400   ATP dependent RNA helicase DOB1
Echinococcus granulosus EgrG_000653300   superkiller viralicidic activity 2 2
Entamoeba histolytica EHI_134610   DEAD/DEAH box helicase, putative
Echinococcus multilocularis EmuJ_000456400   ATP dependent RNA helicase DOB1
Echinococcus multilocularis EmuJ_000653300   superkiller viralicidic activity 2 2
Giardia lamblia GL50803_17146   Helicase
Homo sapiens ENSG00000039123   superkiller viralicidic activity 2-like 2 (S. cerevisiae)
Leishmania braziliensis LbrM.35.3220   ATP-dependent RNA helicase, putative
Leishmania donovani LdBPK_363150.1   ATP-dependent RNA helicase, putative
Leishmania infantum LinJ.36.3150   ATP-dependent RNA helicase, putative
Leishmania major LmjF.36.3000   ATP-dependent RNA helicase, putative
Leishmania mexicana LmxM.36.3000   ATP-dependent RNA helicase, putative
Loa Loa (eye worm) LOAG_06429   hypothetical protein
Mycobacterium leprae ML1333   PROBABLE ATP-DEPENDENT DNA HELICASE HELY
Mus musculus ENSMUSG00000016018   superkiller viralicidic activity 2-like 2 (S. cerevisiae)
Mycobacterium tuberculosis Rv2092c   ATP-dependent DNA helicase HelY
Mycobacterium ulcerans MUL_2324   ATP-dependent DNA helicase HelY
Neospora caninum NCLIV_013510   DEAD/DEAH box helicase family protein, related
Oryza sativa 4349924   Os11g0176200
Oryza sativa 4330670   Os02g0739000
Oryza sativa 9268439   Os12g0279000
Plasmodium berghei PBANKA_0100900   ATP-dependent RNA helicase, putative
Plasmodium falciparum PF3D7_0602100   ATP-dependent RNA helicase, putative
Plasmodium knowlesi PKNH_1148600   ATP-dependant RNA helicase, putative
Plasmodium vivax PVX_113270   ATP-dependent RNA helicase, putative
Plasmodium yoelii PY01861   Homo sapiens KIAA0052 protein-related
Saccharomyces cerevisiae YJL050W   ATP-dependent RNA helicase MTR4
Schistosoma japonicum Sjp_0313730   Superkiller viralicidic activity 2-like 2, putative
Schistosoma japonicum Sjp_0056690   ko:K01529 SKIV2L2; superkiller viralicidic activity 2-like 2 [EC:3.6.1.-], putative
Schistosoma japonicum Sjp_0112830   Uncharacterized helicase C6F12.16c, putative
Schistosoma japonicum Sjp_0113940   Superkiller viralicidic activity 2-like 2, putative
Schistosoma mansoni Smp_120360   helicase
Schistosoma mansoni Smp_059250   helicase
Schmidtea mediterranea mk4.047824.00  
Schmidtea mediterranea mk4.000260.11   mRNA transport homolog 4
Schmidtea mediterranea mk4.039813.01  
Schmidtea mediterranea mk4.010718.01  
Schmidtea mediterranea mk4.000260.10  
Schmidtea mediterranea mk4.039813.00   Uncharacterized helicase
Schmidtea mediterranea mk4.010718.00   Uncharacterized helicase
Trypanosoma brucei gambiense Tbg972.10.9120   ATP-dependent DEAD/H RNA helicase, putative,ATP- dependent RNA helicase, putative
Trypanosoma brucei Tb927.10.7440   ATP-dependent RNA helicase MTR4
Trypanosoma congolense TcIL3000_10_6410   ATP-dependent DEAD/H RNA helicase, putative
Trypanosoma cruzi TcCLB.510105.9   ATP-dependent DEAD/H RNA helicase, putative
Toxoplasma gondii TGME49_213770   Superkiller viralicidic activity 2 family 2, putative
Theileria parva TP02_0517   hypothetical protein
Trichomonas vaginalis TVAG_411940   activating signal cointegrator 1 complex subunit 3, helc1, putative
Trichomonas vaginalis TVAG_309850   conserved hypothetical protein

Essentiality

LmjF.36.3000 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.7440 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.10.7440 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.7440 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.7440 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_W08D2.7 Caenorhabditis elegans embryonic lethal wormbase
CELE_W08D2.7 Caenorhabditis elegans larval arrest wormbase
CELE_W08D2.7 Caenorhabditis elegans slow growth wormbase
CELE_W08D2.7 Caenorhabditis elegans sterile wormbase
YJL050W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0100900 Plasmodium berghei Essential plasmo
TGME49_213770 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.
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
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

111 literature references were 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 LmjF.36.3000 (Leishmania major), ATP-dependent RNA helicase, putative
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