Detailed view for LmjF.33.0520

Basic information

TDR Targets ID: 29867
Leishmania major, d-xylulose reductase, putative

Source Database / ID:  TriTrypDB  GeneDB

pI: 6.2763 | Length (AA): 349 | MW (Da): 37591 | 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

PF00107   Zinc-binding dehydrogenase
PF08240   Alcohol dehydrogenase GroES-like domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005488   binding  
GO:0003824   catalytic activity  
GO:0016491   oxidoreductase activity  
GO:0008270   zinc ion binding  
GO:0008152   metabolic process  
GO:0055114   oxidation reduction  

Metabolic Pathways

Structural information

Modbase 3D models:

There are 7 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
1 349 1yqd (A) 8 355 20.00 0 1 1.2 -0.43
3 349 1e3j (A) 5 351 39.00 0 1 1.52 -1.2
6 348 1pl8 (A) 10 350 42.00 0 1 1.58 -1.13
4 348 1pl8 (A) 8 350 41.00 0 1 1.53194 -0.78
4 349 1rjw (A) 1 338 26.00 0 1 1.2898 -0.13
6 345 1e3j (A) 7 347 41.00 0 1 1.51291 -0.6
49 88 5a3v (A) 53 93 45.00 0.49 0.32 0.441313 1.24

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. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Lower 0-20% 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_126928)

Species Accession Gene Product
Arabidopsis thaliana AT5G51970   putative sorbitol dehydrogenase
Candida albicans CaO19.769   likely Zinc-binding dehydrogenase, one of two genes similar to S. cerevisiae YAL061W and BDH1 (YAL060W) butanediol dehydrogenase
Candida albicans CaO19.7676   similar to P.stipitis xylitol dehydrogenase (XYL2), and to S. cerevisiae SOR1 (YJR159W) sorbitol dehydrogenase
Caenorhabditis elegans CELE_R04B5.6   Protein R04B5.6
Caenorhabditis elegans CELE_R04B5.5   Protein R04B5.5
Drosophila melanogaster Dmel_CG1982   Sorbitol dehydrogenase 1
Drosophila melanogaster Dmel_CG4649   Sorbitol dehydrogenase-2
Escherichia coli b1774   putative Zn-dependent NAD(P)-binding oxidoreductase
Escherichia coli b2091   galactitol-1-phosphate dehydrogenase, Zn-dependent and NAD(P)-binding
Escherichia coli b3616   L-threonine 3-dehydrogenase, NAD(P)-binding
Escherichia coli b4267   L-idonate 5-dehydrogenase, NAD-binding
Escherichia coli b1776   putative Zn-dependent NAD(P)-binding oxidoreductase
Entamoeba histolytica EHI_023110   NADP-dependent alcohol dehydrogenase
Homo sapiens 6652   sorbitol dehydrogenase
Leishmania braziliensis LbrM.33.0520   d-xylulose reductase, putative
Leishmania donovani LdBPK_330530.1   d-xylulose reductase, putative
Leishmania infantum LinJ.33.0530   d-xylulose reductase, putative
Leishmania major LmjF.33.0520   d-xylulose reductase, putative
Leishmania mexicana LmxM.32.0520   d-xylulose reductase, putative
Loa Loa (eye worm) LOAG_12517   hypothetical protein
Mus musculus ENSMUSG00000027227   sorbitol dehydrogenase
Mycobacterium ulcerans MUL_0819   short-chain dehydrogenase
Oryza sativa 4346217   Os08g0545200
Saccharomyces cerevisiae YAL061W   putative dehydrogenase BDH2
Saccharomyces cerevisiae YJR159W   L-iditol 2-dehydrogenase SOR1
Saccharomyces cerevisiae YAL060W   (R,R)-butanediol dehydrogenase
Saccharomyces cerevisiae YDL246C   L-iditol 2-dehydrogenase SOR2
Saccharomyces cerevisiae YLR070C   D-xylulose reductase XYL2
Schmidtea mediterranea mk4.002176.02  
Schmidtea mediterranea mk4.002176.01  

Essentiality

LmjF.33.0520 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b1774 Escherichia coli non-essential goodall
b1776 Escherichia coli non-essential goodall
b2091 Escherichia coli non-essential goodall
b3616 Escherichia coli non-essential goodall
b4267 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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

Druggability index (range: 0 to 1): 0.9


Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Rattus norvegicus Sorbitol dehydrogenase Compounds References
Homo sapiens sorbitol dehydrogenase Compounds References
By sequence similarity to non orthologous druggable targets
Species Target Length Identity Alignment span Linked Drugs Reference
Rhodobacter capsulatus 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A dehydrogenase 314 aa 22.5% 325 aa Compounds References

Obtained from network model

Ranking Plot


Putative Drugs List


Compound Raw Global Species
0.0067 0.4566 1
0.0969 1 1
0.0707 1 1
0.0608 1 1
0.0614 1 1
0.0067 1 1
0.0613 0.4221 1
0.0806 1 1
0.0242 0.3416 0.3348
0.0664 0.8299 1
0.0134 1 1
0.0613 0.4221 1
0.041 1 1
0.0664 0.8299 1
0.0601 1 1
0.0067 1 1
0.0126 0.4454 1
0.0067 1 0.5
0.0625 1 1
0.0405 1 1
0.0244 0.5462 1
0.0664 0.8299 1
0.0526 1 1
0.0067 0.3009 0.8768
0.0656 1 1
0.0134 1 1
0.0113 1 1
0.076 1 1
0.0134 1 1
0.0806 1 1
0.0125 1 1
0.0111 1 1
0.0229 1 1
0.0067 1 1
0.0404 1 1
0.0111 1 1
0.0401 1 1
0.0134 1 1
0.0228 1 1
0.0384289 0.366107 1
0.0808 1 1
0.0282 1 1
0.0338 1 1
0.0505 0.4106 0.7676
0.0405 1 1
0.0714 1 1
0.0343 1 1
0.0134 1 1
0.0067 1 1
0.0177 1 1
0.0601 1 1
0.0221 0.2559 0.6658
0.0622 1 1
0.0405 1 1
0.0067 0.2709 0.2666
0.0186 0.6864 1
0.0232 0.8761 1
0.0608 1 1
0.0067 0.6675 1
0.0129 1 1
0.0608 1 1
0.0234 1 1
0.0242 0.3416 0.3348
0.0067 1 1
0.0664 0.8299 1
0.0408 1 1
0.0281 1 1
0.0969 1 1
0.0054 1 1
0.0126 1 1

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.33.0520 (Leishmania major), d-xylulose reductase, putative
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