Detailed view for LmjF.24.1820

Basic information

TDR Targets ID: 21253
Leishmania major, short chain dehydrogenase/reductase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.8951 | Length (AA): 507 | MW (Da): 54629 | Paralog Number: 0

Signal peptide: Y | 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

PF00106   short chain dehydrogenase

Gene Ontology

Mouse over links to read term descriptions.
GO:0016491   oxidoreductase activity  
GO:0005488   binding  
GO:0003824   catalytic activity  
GO:0008152   metabolic process  

Metabolic Pathways

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

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
168 498 1w6u (A) 48 328 16.00 0 1 0.64 0.3
169 507 1yxm (A) 8 300 17.00 0 0.94 0.55 0.43
175 345 1yb1 (A) 27 174 31.00 0.00000025 1 0.59 -0.37
167 500 3rd5 (A) 2 284 29.00 0 1 0.696877 0.22
176 219 1hdc (A) 3 46 34.00 0 0.93 0.483685 -0.31
176 246 5g4k (A) 14 84 17.00 0 0.5 0.352939 -0.6
184 288 4fc7 (A) 33 114 46.00 0.076 0.95 0.379701 0.74

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_137346)

Species Accession Gene Product
Caenorhabditis elegans CELE_K10H10.6   Protein K10H10.6
Caenorhabditis elegans CELE_K10H10.3   Protein DHS-8, isoform A
Leishmania braziliensis LbrM.24.1890   short chain dehydrogenase/reductase, putative
Leishmania donovani LdBPK_241890.1   short chain dehydrogenase/reductase, putative
Leishmania infantum LinJ.24.1890   short chain dehydrogenase/reductase, putative
Leishmania major LmjF.24.1820   short chain dehydrogenase/reductase, putative
Leishmania mexicana LmxM.24.1820   short chain dehydrogenase/reductase, putative
Trypanosoma brucei gambiense Tbg972.8.6470   short-chain dehydrogenase, putative
Trypanosoma brucei Tb927.8.6410   beta-ketoacyl-ACP reductase 3, putative
Trypanosoma congolense TcIL3000_8_6260   short-chain dehydrogenase, putative
Trypanosoma cruzi TcCLB.511907.70   short chain dehydrogenase/reductase, putative
Trypanosoma cruzi TcCLB.506797.90   short chain dehydrogenase/reductase, putative

Essentiality

LmjF.24.1820 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.6410 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.8.6410 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.8.6410 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.8.6410 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection

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
Species Target Length Identity Alignment span Linked Drugs Reference
Macaca mulatta Hydroxysteroid 11-beta dehydrogenase 1 140 aa 26.1% 161 aa Compounds References
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0032 1 1
0.0157 0.5 0.5
0.008 0.5 0.5
0.0053 1 1
0.0056 1 1
0.0085 1 1
0.0088 1 1
0.0089 0.5 0.5
0.0073 0.4546 1
0.0102 0.7451 0.5
0.0402 1 1
0.007 1 1
0.0009 1 0.5
0.0035 1 1
0.0009 0.5 0.5
0.007 0.2916 1
0.0039 1 1
0.0106 1 0.5
0.0009 0.5 0.5
0.0013 0.5 0.5
0.0027 0.5 0.5
0.0046 0.3082 0
0.0058 1 1
0.0009 0.5 0.5
0.0114 1 1
0.0058 0.3931 1
0.0004 0.5 0.5
0.016 0.577 1
0.0005 0.5 0.5
0.0076 1 1
0.016 0.577 1
0.0013 1 0.5
0.0408 0.5144 1
0.0088 0.6544 1
0.0012 0.5 0.5
0.0089 0.5 0.5
0.0004 0.5 0.5
0.0119 0.2746 1
0.0222 0.5 0.5
0.0132 0.3658 1
0.0004 0.5 0.5
0.0118 1 1
0.0066 0.3586 0.5
0.0165 1 1
0.0064 0.3508 0.5
0.0021 0.5 0.5
0.0071 0.3141 0
0.0057 0.284 0.6352
0.0123 0.5 0.5
0.0056 0.875 1
0.0408 0.5144 1
0.0005 0.5 0.5
0.0106 0.5 0.5
0.0408 0.5144 1
0.0068 0.2585 0.5
0.007 1 1
0.0004 0.5 0.5
0.0087 0.5 0.5
0.0073 0.3141 1
0.0113 1 1
0.0097 1 1
0.0162 1 1
0.0045 1 1
0.0019 0.4322 1
0.0084 0.4283 0.4047
0.0108 0.5 0.5
0.0009 0.5 0.5
0.0171 0.4063 0.5
0.0097 0.4304 1
0.0131 0.5 0.5
0.0196 0.8679 0.5
0.0009 0.5 0.5
0.0027 0.5 0.5
0.007 0.2916 1
0.0218 0.5 0.5
0.007 0.2916 1
0.0068 1 1
0.0067 0.3468 1
0.0114 1 1
0.0106 1 1
0.0106 0.2872 1
0.0171 0.4063 0.5
0.0009 0.5 0.5
0.0073 0.2873 0.4086
0.004 0.5 0.5
0.0196 0.8679 0.5
0.0009 0.7374 0.5
0.0073 0.3811 1
0.011 0.3568 0.5973
0.0012 0.5 0.5
0.0004 0.5 0.5
0.0004 0.5 0.5
0.0026 0.5 0.5
0.0073 0.3811 1
0.0082 1 0.5
0.0016 0.5 0.5
0.0004 0.5 0.5
0.0053 1 1
0.0196 0.8679 0.5
0.0009 0.5 0.5
0.0009 0.5 0.5
0.0068 1 1
0.0021 0.3321 0.5
0.0093 0.5 0.5
0.0021 0.3321 0.5
0.007 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.24.1820 (Leishmania major), short chain dehydrogenase/reductase, putative
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