Detailed view for LmjF.36.6340

Basic information

TDR Targets ID: 26865
Leishmania major, ubiquitin-protein ligase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.3535 | Length (AA): 4165 | MW (Da): 454856 | 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)
PF13385   Concanavalin A-like lectin/glucanases superfamily

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 17 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
3354 3529 2fbe (A) 6 183 12.00 0 0.22 -0.18 -0.11
3727 4125 1zvd (A) 369 741 23.00 0 1 0.31 -0.22
3754 4124 1nd7 (A) 565 914 25.00 0.0000000000031 1 0.31 -0.32
416 603 3pvn (A) 5 199 17.00 0 0.92 0.0592381 0.15
418 576 1pz7 (A) 13 193 16.00 0 0.79 0.0232753 0.11
1549 1693 2yyo (A) 15 163 37.00 0 1 0.465914 -0.79
1578 1698 5ji7 (A) 215 336 34.00 0 1 0.482752 -0.43
2030 2272 3uzu (A) 48 274 29.00 0.29 0.92 0.206043 0.75
2303 2347 5chl (A) 24 68 22.00 0 0.01 0.239904 -0.41
2383 2560 1qu0 (A) 2938 3108 22.00 0 0.75 0.146837 0.18
2712 2871 5e09 (A) 84 226 28.00 0.45 0.47 0.206115 0.2
3386 3549 4p9j (C) 1071 1229 25.00 0 0.96 0.277476 -0.75
3396 3548 4p9j (C) 1083 1228 32.00 0.00000000048 1 0.346435 -0.49
3399 3552 4xw3 (A) 131 265 33.00 0.00026 0.86 0.140675 0.13
3727 4124 3h1d (A) 4001 4365 23.00 0 1 0.177658 0.45
3790 4125 5c91 (A) 572 892 29.00 0 1 0.289372 0.62
4045 4124 3pt3 (A) 2709 2792 29.00 0.13 0.91 0.258608 -0.62

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_140579)

Species Accession Gene Product
Leishmania braziliensis LbrM.35.6640   ubiquitin-protein ligase, putative
Leishmania donovani LdBPK_366600.1   ubiquitin-protein ligase, putative
Leishmania infantum LinJ.36.6600   ubiquitin-protein ligase, putative
Leishmania major LmjF.36.6340   ubiquitin-protein ligase, putative
Leishmania mexicana LmxM.36.6340   ubiquitin-protein ligase, putative
Trypanosoma brucei gambiense Tbg972.10.10220   hypothetical protein, conserved
Trypanosoma brucei Tb927.10.8390   Concanavalin A-like lectin/glucanases superfamily/SPRY domain/HECT-domain (ubiquitin-transferase), putative
Trypanosoma congolense TcIL3000_10_7230   Concanavalin A-like lectin/glucanases superfamily, putative
Trypanosoma congolense TcIL3000_10_7240   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.508231.60   ubiquitin-protein ligase, putative

Essentiality

LmjF.36.6340 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.8390 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.10.8390 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.8390 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.8390 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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.
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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

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): 0.5

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.36.6340 (Leishmania major), ubiquitin-protein ligase, putative
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