Detailed view for LmjF.35.4670

Basic information

TDR Targets ID: 26900
Leishmania major, katanin, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.3455 | Length (AA): 589 | MW (Da): 64556 | 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

PF12894   Anaphase-promoting complex subunit 4 WD40 domain
PF13925   con80 domain of Katanin

Gene Ontology

Mouse over links to read term descriptions.
GO:0005515   protein binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 5 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
2 334 2h14 (A) 35 334 17.00 0 1 0.64 -0.06
5 284 1got (B) 48 340 18.00 0 1 0.78 -0.95
50 399 2ymu (A) 135 486 23.00 0.000000000042 1 0.793028 0.43
95 212 5cyk (A) 223 420 37.00 0.0087 0.93 0.11414 0.41
95 251 4wju (A) 141 308 29.00 0.000000072 1 0.658354 -0.9

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_129945)

Species Accession Gene Product
Arabidopsis thaliana AT5G08390   transducin/WD40 repeat-like superfamily protein
Arabidopsis thaliana AT1G61210   protein DWD hypersensitive to ABA 3
Arabidopsis thaliana AT5G23430   Katanin p80 WD40 repeat-containing subunit B1-1
Arabidopsis thaliana AT1G11160   WD40 domain-containing protein
Drosophila melanogaster Dmel_CG13956   katanin 80
Echinococcus granulosus EgrG_000480700   katanin p80 WD40 containing subunit B1
Echinococcus multilocularis EmuJ_000480700   katanin p80 WD40 containing subunit B1
Homo sapiens ENSG00000140854   katanin p80 (WD repeat containing) subunit B 1
Leishmania braziliensis LbrM.34.4650   katanin, putative
Leishmania donovani LdBPK_354740.1   katanin, putative
Leishmania infantum LinJ.35.4740   katanin, putative
Leishmania major LmjF.35.4670   katanin, putative
Leishmania mexicana LmxM.34.4670   katanin, putative
Mus musculus ENSMUSG00000031787   katanin p80 (WD40-containing) subunit B 1
Oryza sativa 4348995   Os10g0494800
Oryza sativa 4327835   Os01g0780400
Oryza sativa 4337408   Os04g0677700
Schistosoma japonicum Sjp_0087640   Katanin p80 WD40-containing subunit B1, putative
Schmidtea mediterranea mk4.009235.03   Putative katanin P80 subunit
Schmidtea mediterranea mk4.009235.04   Putative katanin P80 subunit
Schmidtea mediterranea mk4.010406.00   Putative katanin P80 subunit
Trypanosoma brucei gambiense Tbg972.9.5740   katanin, putative
Trypanosoma brucei Tb927.9.9960   katanin, putative
Trypanosoma congolense TcIL3000_9_3630   katanin, putative
Trypanosoma cruzi TcCLB.506887.50   katanin, putative
Trypanosoma cruzi TcCLB.510731.40   katanin, putative
Trichomonas vaginalis TVAG_130970   G-protein beta WD- 40 repeats containing protein, putative
Trichomonas vaginalis TVAG_397060   katanin P80 subunit, putative
Trichomonas vaginalis TVAG_230250   WD-repeat protein, putative
Trichomonas vaginalis TVAG_499000   katanin P80 subunit, putative
Trichomonas vaginalis TVAG_363890   katanin P80 subunit, putative
Trichomonas vaginalis TVAG_165010   katanin P80 subunit, putative

Essentiality

LmjF.35.4670 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.1500 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.211.1500 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.211.1500 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb09.211.1500 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84

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

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.35.4670 (Leishmania major), katanin, putative
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