Detailed view for LmjF.13.1470

Basic information

TDR Targets ID: 21660
Leishmania major, hypothetical protein, conserved
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.935 | Length (AA): 5636 | MW (Da): 593231 | 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

PF00622   SPRY domain
PF00632   HECT-domain (ubiquitin-transferase)

Gene Ontology

Mouse over links to read term descriptions.
GO:0005622   intracellular  
GO:0016881   acid-amino acid ligase activity  
GO:0005515   protein binding  
GO:0004842   ubiquitin-protein ligase activity  
GO:0006464   protein modification process  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 19 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
5036 5464 1nd7 (A) 546 915 24.00 0 1 0.18 0.13
5065 5464 1zvd (A) 388 741 25.00 0 1 0.3 -0.1
29 204 2jk9 (A) 37 227 16.00 0 0.38 0.0596278 -0.2
30 201 3emw (A) 27 214 16.00 0 0.89 0.0849181 -0.03
31 204 2v24 (A) 36 227 15.00 0 0.82 0.089273 -0.11
449 478 3bog (C) 3 63 53.00 0.51 0.22 0.539423 0.04
3100 3210 2mqa (A) 20 128 17.00 0 0.02 0.0880948 -0.19
4276 4450 3ek9 (A) 26 178 29.00 0.9 0.84 0.14715 0.54
4320 4415 2fnj (A) 81 150 44.00 0.21 0.23 -0.0118666 1.08
4320 4457 2jk9 (A) 77 195 33.00 0.15 0.99 0.0715855 0.78
4327 4525 5c33 (A) 652 841 23.00 0 0.99 -0.00529127 0.45
4608 4747 4p9j (C) 1080 1175 39.00 0.0065 1 -0.0200597 0.71
4610 4747 4p9i (A) 1095 1188 42.00 0.011 0.95 -0.180415 1.06
4642 4744 4qt6 (A) 2054 2160 34.00 0.28 0.99 0.154375 0.79
5035 5416 5hps (A) 545 885 28.00 0.00000043 1 0.126879 0.87
5058 5452 5c7m (A) 533 898 21.00 0 1 0.140785 0.51
5076 5412 3g1n (B) 4023 4331 28.00 0 1 0.170194 0.45
5388 5503 2qtw (B) 532 674 11.00 0 0.07 0.042982 -0.1
5513 5592 3pt3 (A) 2714 2791 33.00 0.084 0.22 0.0878945 -0.3

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
Lower 20-40% 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_140406)

Species Accession Gene Product
Dictyostelium discoideum DDB_G0286931   hypothetical protein
Leishmania braziliensis LbrM.13.1230   hypothetical protein, conserved
Leishmania donovani LdBPK_131520.1   SPRY domain/HECT-domain (ubiquitin-transferase), putative
Leishmania infantum LinJ.13.1520   hypothetical protein, conserved
Leishmania major LmjF.13.1470   hypothetical protein, conserved
Leishmania mexicana LmxM.13.1470   hypothetical protein, conserved
Trypanosoma brucei gambiense Tbg972.11.3830   hypothetical protein, conserved
Trypanosoma brucei Tb927.11.3390   Concanavalin A-like lectin/glucanases superfamily/SPRY domain/HECT-domain (ubiquitin-transferase), putative
Trypanosoma congolense TcIL3000.11.3280   Concanavalin A-like lectin/glucanases superfamily/SPRY domain/HECT-domain (ubiquitin-transferase), putative
Trypanosoma cruzi TcCLB.507099.40   Concanavalin A-like lectin/glucanases superfamily/SPRY domain/HECT-domain (ubiquitin-transferase), putative

Essentiality

LmjF.13.1470 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.02.0880 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.02.0880 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.02.0880 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.02.0880 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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): 0.3

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.

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Gene identifier LmjF.13.1470 (Leishmania major), hypothetical protein, conserved
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