Detailed view for LmjF.28.0400

Basic information

TDR Targets ID: 28109
Leishmania major, katanin, putative,serine peptidase, Clan SJ, family S16, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 9.3005 | Length (AA): 547 | MW (Da): 59637 | 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:0051013   microtubule severing  
GO:0008568   microtubule-severing ATPase activity  
GO:0008017   microtubule binding  
GO:0005524   ATP binding  
GO:0000166   nucleotide binding  
GO:0017111   nucleoside-triphosphatase activity  

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
98 523 1e32 (A) 35 458 25.00 0 1 0.98 0.09
253 545 1xwi (A) 124 442 46.00 0 1 1.06 -0.88
260 503 2ce7 (A) 158 401 36.00 0 1 0.97 -1.33
3 74 2rpa (A) 0 72 28.00 0.000000000072 0.89 0.559227 -0.77
7 224 4tql (A) 10 234 7.00 0.21 0 0.438137 -0.08
67 544 5c19 (D) 268 763 26.00 0.000018 1 1.05946 0.96
244 539 3b9p (A) 464 749 47.00 0 1 0.975833 -0.03
260 503 3whk (A) 178 422 37.00 0 1 0.886769 -0.69
435 523 2dzn (D) 348 413 26.00 0 0.72 0.132206 -0.14

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 60-80% percentile metacyclic. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile amastigotes. 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_128745)

Species Accession Gene Product
Arabidopsis thaliana AT1G80350   ATPase katanin p60
Brugia malayi Bm1_36115   ATPase, AAA family protein
Caenorhabditis elegans CELE_T01G9.5   Protein MEI-1, isoform B
Drosophila melanogaster Dmel_CG10229   Katanin 60
Echinococcus granulosus EgrG_000108700   katanin p60 ATPase containing subunit A1
Echinococcus multilocularis EmuJ_000108700   katanin p60 ATPase containing subunit A1
Giardia lamblia GL50803_15368   Katanin
Homo sapiens ENSG00000102781   katanin p60 subunit A-like 1
Homo sapiens ENSG00000186625   katanin p60 (ATPase containing) subunit A 1
Leishmania braziliensis LbrM.28.0410   katanin, putative,serine peptidase, Clan SJ, family S16, putative
Leishmania donovani LdBPK_280390.1   katanin, putative
Leishmania infantum LinJ.28.0390   katanin, putative,serine peptidase, Clan SJ, family S16, putative
Leishmania major LmjF.28.0400   katanin, putative,serine peptidase, Clan SJ, family S16, putative
Leishmania mexicana LmxM.28.0400   katanin, putative,serine peptidase, Clan SJ, family S16, putative
Loa Loa (eye worm) LOAG_05708   ATPase
Mus musculus ENSMUSG00000019794   katanin p60 (ATPase-containing) subunit A1
Mus musculus 231912   katanin p60 subunit A-like 1
Neospora caninum NCLIV_019140   p60 katanin, putative
Oryza sativa 4324404   Os01g0683100
Schistosoma japonicum Sjp_0208420   ko:K07767 microtubule-severing ATPase [EC3.6.4.3], putative
Schistosoma mansoni Smp_126110   hypothetical protein
Schmidtea mediterranea mk4.002295.02  
Trypanosoma brucei gambiense Tbg972.11.9530   katanin, putative,serine peptidase, Clan SJ, family S16, putative
Trypanosoma brucei gambiense Tbg972.10.1170   katanin, putative
Trypanosoma brucei Tb11.v5.0486   katanin, putative
Trypanosoma brucei Tb927.11.8350   katanin, putative
Trypanosoma brucei Tb927.10.1210   katanin, putative
Trypanosoma congolense TcIL3000_10_1010   katanin, putative
Trypanosoma congolense TcIL3000.11.8890   katanin, putative
Trypanosoma congolense TcIL3000_0_36140   katanin, putative
Trypanosoma cruzi TcCLB.509695.50   katanin, putative
Trypanosoma cruzi TcCLB.509967.70   katanin, putative
Trypanosoma cruzi TcCLB.506163.80   katanin, putative
Toxoplasma gondii TGME49_244590   katanin-like family protein
Trichomonas vaginalis TVAG_498860   AAA ATPase, putative
Trichomonas vaginalis TVAG_028490   AAA ATPase, putative
Trichomonas vaginalis TVAG_245050   AAA ATPase, putative

Essentiality

LmjF.28.0400 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.1210 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.1210 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.1210 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.1210 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Tb11.01.0200 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.01.0200 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.0200 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.01.0200 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_T01G9.5 Caenorhabditis elegans embryonic lethal wormbase
TGME49_244590 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.

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.

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User comments

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Gene identifier LmjF.28.0400 (Leishmania major), katanin, putative,serine peptidase, Clan SJ, family S16, putative
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