Detailed view for LmjF.13.0960

Basic information

TDR Targets ID: 28106
Leishmania major, katanin-like protein,serine peptidase, Clan SJ, family S16, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.8053 | Length (AA): 565 | MW (Da): 61445 | 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)
PF09336   Vps4 C terminal oligomerisation domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0017111   nucleoside-triphosphatase activity  
GO:0005524   ATP binding  
GO:0005515   protein binding  
GO:0000166   nucleotide binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 10 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
101 539 1e32 (A) 43 458 25.00 0 1 0.8 0.38
271 512 1d2n (A) 505 748 18.00 0 0.98 0.57 -0.93
274 560 1xwi (A) 129 441 48.00 0 1 1.04 -0.76
43 81 5en8 (A) 11 46 53.00 0.1 0.6 0.549727 0.19
247 562 3d8b (A) 376 673 42.00 0 1 0.890192 0.14
258 557 5ifw (B) 456 760 38.00 0 1 0.809673 0.51
260 561 4l15 (A) 297 586 41.00 0 1 0.993413 -0.48
267 561 3eih (A) 121 434 46.00 0 1 1.02102 -0.5
270 500 4ww0 (A) 146 379 39.00 0 1 0.83655 -0.38
453 500 2dzn (D) 349 397 35.00 0 0.85 0.454856 0.19

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. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Upper 60-80% 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_130102)

Species Accession Gene Product
Arabidopsis thaliana AT2G34560   nucleoside triphosphatase CCP1
Drosophila melanogaster Dmel_CG10793   CG10793 gene product from transcript CG10793-RA
Echinococcus granulosus EgrG_000356500   katanin p60 ATPase containing subunit
Echinococcus multilocularis EmuJ_000356500   katanin p60 ATPase containing subunit
Giardia lamblia GL50803_10361   P60 katanin
Homo sapiens ENSG00000167216   katanin p60 subunit A-like 2
Leishmania braziliensis LbrM.13.0770   katanin-like protein,serine peptidase, Clan SJ, family S16, putative
Leishmania donovani LdBPK_130850.1   katanin-like protein
Leishmania infantum LinJ.13.0850   katanin-like protein,serine peptidase, Clan SJ, family S16, putative
Leishmania major LmjF.13.0960   katanin-like protein,serine peptidase, Clan SJ, family S16, putative
Leishmania mexicana LmxM.13.0960   katanin-like protein,serine peptidase, Clan SJ, family S16, putative
Mus musculus ENSMUSG00000025420   katanin p60 subunit A-like 2
Oryza sativa 4325904   Os01g0673500
Oryza sativa 4325146   Os01g0757400
Schistosoma japonicum Sjp_0033340   Katanin p60 ATPase-containing subunit A-like 2, putative
Schistosoma japonicum Sjp_0104630   Katanin p60 ATPase-containing subunit A-like 2, putative
Schistosoma mansoni Smp_140150   hypothetical protein
Schmidtea mediterranea mk4.000037.14  
Trypanosoma brucei gambiense Tbg972.11.4490   katanin, putative
Trypanosoma brucei Tb927.11.3870   katanin, putative
Trypanosoma congolense TcIL3000.11.3840   serine peptidase, Clan SJ, family S16, putative
Trypanosoma cruzi TcCLB.511857.59   katanin, putative
Trypanosoma cruzi TcCLB.506733.40   katanin-like protein, putative
Trichomonas vaginalis TVAG_109940   mei-1, putative
Trichomonas vaginalis TVAG_174770   mei-1, putative

Essentiality

LmjF.13.0960 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.02.1370 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.02.1370 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.02.1370 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.02.1370 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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.
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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.
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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

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

Druggability index (range: 0 to 1): 0.2

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.13.0960 (Leishmania major), katanin-like protein,serine peptidase, Clan SJ, family S16, putative
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