Detailed view for LmjF.13.1090

Basic information

TDR Targets ID: 22960
Leishmania major, proteasome regulatory ATPase subunit 2, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.6015 | Length (AA): 438 | MW (Da): 49289 | 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

PF00004   ATPase family associated with various cellular activities (AAA)

Gene Ontology

Mouse over links to read term descriptions.
GO:0036402   GO:proteasome-activating ATPase activity  

GO:0005737   cytoplasm  
GO:0005634   nucleus  
GO:0005524   ATP binding  
GO:0000166   nucleotide binding  
GO:0017111   nucleoside-triphosphatase activity  
GO:0016787   hydrolase activity  
GO:0030163   protein catabolic process  

Metabolic Pathways

Proteasome (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
4 436 1e32 (A) 29 452 29.00 0 1 1.25 0.1
181 424 1lv7 (A) 153 395 40.00 0 1 1.13 -1.06
24 438 5c18 (A) 319 757 28.00 0.026 1 1.22219 0.51
172 431 3h4m (A) 159 418 57.00 0.0013 1 1.36031 -1.21
354 428 4a3v (B) 380 454 31.00 0 0.62 0.645133 -1.33
359 420 2dzn (D) 349 410 40.00 0 1 0.690453 -0.8

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 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_127456)

Species Accession Gene Product
Arabidopsis thaliana AT4G29040   regulatory particle AAA-ATPase 2A
Arabidopsis thaliana AT2G20140   26S proteasome subunit RPT2B
Babesia bovis BBOV_IV009290   26S protease regulatory subunit 4, putative
Brugia malayi Bm1_52520   Probable 26S protease regulatory subunit 4
Candida albicans CaO19.5440   likely ATPase similar to S. cerevisiae RPT2 (YDL007W) ATPase subunit of the 19S regulatory particle of the 26S proteasome
Candida albicans CaO19.12895   likely ATPase similar to S. cerevisiae RPT2 (YDL007W) ATPase subunit of the 19S regulatory particle of the 26S proteasome
Caenorhabditis elegans CELE_F29G9.5   Protein RPT-2
Cryptosporidium hominis Chro.40138   26S proteasome AAA-ATPase subunit RPT2a
Cryptosporidium parvum cgd4_1170   26S proteasome regulatory subunit S4 like AAA ATpase
Dictyostelium discoideum DDB_G0270784   26S protease regulatory subunit 4
Drosophila melanogaster Dmel_CG5289   Regulatory particle triple-A ATPase 2
Echinococcus granulosus EgrG_001101900   proteasome 26s subunit subunit 4 atpase
Entamoeba histolytica EHI_180350   26S protease regulatory subunit, putative
Echinococcus multilocularis EmuJ_001101900   proteasome 26s subunit subunit 4 atpase
Giardia lamblia GL50803_113554   26S proteasome ATPase subunit S4, putative
Homo sapiens ENSG00000100764   proteasome (prosome, macropain) 26S subunit, ATPase, 1
Leishmania braziliensis LbrM.13.0890   proteasome regulatory ATPase subunit 2, putative
Leishmania donovani LdBPK_130990.1   proteasome regulatory ATPase subunit 2, putative
Leishmania infantum LinJ.13.0990   proteasome regulatory ATPase subunit 2, putative
Leishmania major LmjF.13.1090   proteasome regulatory ATPase subunit 2, putative
Leishmania mexicana LmxM.13.1090   proteasome regulatory ATPase subunit 2, putative
Loa Loa (eye worm) LOAG_00367   RPT-2 protein
Mus musculus ENSMUSG00000021178   protease (prosome, macropain) 26S subunit, ATPase 1
Oryza sativa 4344373   Os07g0691800
Oryza sativa 4332553   Os03g0298400
Plasmodium berghei PBANKA_1206600   26S protease regulatory subunit 4, putative
Plasmodium falciparum PF3D7_1008400   26S protease regulatory subunit 4, putative
Plasmodium knowlesi PKNH_0807400   26S protease regulatory subunit 4, putative
Plasmodium vivax PVX_094615   26S protease regulatory subunit 4, putative
Plasmodium yoelii PY00768   26S proteasome subunit 4-like protein
Saccharomyces cerevisiae YDL007W   proteasome regulatory particle base subunit RPT2
Schistosoma japonicum Sjp_0210920   ko:K01509 adenosinetriphosphatase [EC3.6.1.3], putative
Schistosoma mansoni Smp_173840   26S protease regulatory subunit
Schmidtea mediterranea mk4.028015.01   26S protease regulatory subunit 4
Schmidtea mediterranea mk4.028015.02   26S protease regulatory subunit 4
Schmidtea mediterranea mk4.002047.06   26S protease regulatory subunit 4
Schmidtea mediterranea mk4.006173.02   26S protease regulatory subunit 4
Schmidtea mediterranea mk4.013821.02   26S protease regulatory subunit 4
Schmidtea mediterranea mk4.001166.04   26S protease regulatory subunit 4
Schmidtea mediterranea mk4.000265.11   26S protease regulatory subunit 4
Schmidtea mediterranea mk4.000265.02   26S protease regulatory subunit 4
Schmidtea mediterranea mk4.004026.01  
Schmidtea mediterranea mk4.001166.00   26S protease regulatory subunit 4
Schmidtea mediterranea mk4.002047.04   26S protease regulatory subunit 4
Schmidtea mediterranea mk4.012837.00   26S protease regulatory subunit 4
Schmidtea mediterranea mk4.001166.01  
Schmidtea mediterranea mk4.010528.01   26S protease regulatory subunit 4
Trypanosoma brucei gambiense Tbg972.11.4280   proteasome regulatory ATPase subunit 2, putative
Trypanosoma brucei Tb927.11.3740   proteasome regulatory ATPase subunit 2
Trypanosoma congolense TcIL3000.11.3690   proteasome regulatory ATPase subunit 2
Trypanosoma cruzi TcCLB.511859.180   proteasome regulatory ATPase subunit 2, putative
Trypanosoma cruzi TcCLB.511047.50   proteasome regulatory ATPase subunit 2, putative
Toxoplasma gondii TGME49_267080   26S protease regulatory subunit 4, putative
Theileria parva TP01_0845   26S proteasome regulatory subunit 4, putative
Trichomonas vaginalis TVAG_074870   26S protease regulatory subunit 6A, putative

Essentiality

LmjF.13.1090 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.02.1220 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.02.1220 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.02.1220 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.02.1220 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F29G9.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_F29G9.5 Caenorhabditis elegans slow growth wormbase
YDL007W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1206600 Plasmodium berghei Essential plasmo
TGME49_267080 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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)

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 proteasome (prosome, macropain) 26S subunit, ATPase, 1 Compounds References
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.

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Gene identifier LmjF.13.1090 (Leishmania major), proteasome regulatory ATPase subunit 2, putative
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