Detailed view for LmjF.30.2770

Basic information

TDR Targets ID: 24162
Leishmania major, superoxide dismutase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.5783 | Length (AA): 268 | MW (Da): 30329 | 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

PF00081   Iron/manganese superoxide dismutases, alpha-hairpin domain
PF02777   Iron/manganese superoxide dismutases, C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0046872   metal ion binding  
GO:0004784   superoxide dismutase activity  
GO:0006801   superoxide metabolic process  
GO:0055114   oxidation reduction  

Metabolic Pathways

Peroxisome (KEGG)

Structural information

Modbase 3D models:

There are 6 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
45 265 1gv3 (A) 29 237 16.00 0 1 1.02 -1.19
53 268 1bsm (A) 1 201 24.00 0 1 1.16 -1.18
55 262 1uer (A) 3 191 23.00 0 1 1.13 -1.52
42 267 4h3e (A) 21 233 25.00 0 1 1.19158 -0.97
55 255 1bsm (A) 3 188 32.00 0.0000000095 0.78 0.9466 -0.15
56 267 2goj (A) 3 196 21.00 0 1 1.06734 -0.95

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 amastigotes. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Mid 40-60% 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_148158)

Species Accession Gene Product
Leishmania braziliensis LbrM.30.2740   superoxide dismutase, putative
Leishmania donovani LdBPK_302780.1   superoxide dismutase, putative
Leishmania infantum LinJ.30.2780   superoxide dismutase, putative
Leishmania major LmjF.30.2770   superoxide dismutase, putative
Leishmania mexicana LmxM.29.2770   superoxide dismutase, putative
Trypanosoma brucei gambiense Tbg972.6.3810   superoxide dismutase, putative
Trypanosoma brucei Tb927.6.4030   superoxide dismutase, putative
Trypanosoma congolense TcIL3000_6_3430   superoxide dismutase, putative
Trypanosoma cruzi TcCLB.511521.30   superoxide dismutase, putative
Trypanosoma cruzi TcCLB.511735.60   superoxide dismutase, putative
Trypanosoma cruzi TcCLB.511737.3   superoxide dismutase, putative

Essentiality

LmjF.30.2770 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.6.4030 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.6.4030 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.6.4030 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.6.4030 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.

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
Species Target Length Identity Alignment span Linked Drugs Reference
Leishmania major iron superoxide dismutase, putative 195 aa 24.0% 192 aa Compounds References
Plasmodium falciparum superoxide dismutase [Fe] 198 aa 21.8% 202 aa Compounds References
Leishmania major iron superoxide dismutase, putative 208 aa 24.8% 202 aa Compounds References
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

  • Assay for Superoxide Dismutase (1.15.1.1 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

No reagent availability information for this target.

Bibliographic References

35 literature references were collected for this gene.

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.30.2770 (Leishmania major), superoxide dismutase, putative
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