Detailed view for Tb927.9.14040

Basic information

TDR Targets ID: 17022
Trypanosoma brucei, short-chain dehydrogenase, putative

Source Database / ID:  TriTrypDB  GeneDB

pI: 8.4798 | Length (AA): 426 | MW (Da): 47381 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 2

Druggability Group : DG4

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:0005575   cellular_component  
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 5 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
34 98 3mje (A) 180 245 32.00 0.32 0.16 0.174582 1.63
65 400 3rd5 (A) 8 286 31.00 0 1 0.810732 0.57
68 162 3ai3 (A) 4 94 31.00 0.00021 1 0.701105 -1.19
72 111 2ekp (A) 3 42 48.00 0.0078 0.97 0.669997 -0.1
255 366 2ntv (A) 155 263 13.00 0.37 0.02 0.233911 1.3

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
Upper 60-80% percentile Procyclic, Bloodstream Form. Siegel TN
Show/Hide expression data references
  • Siegel TN Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites.

Orthologs

Ortholog group members (OG5_132820)

Species Accession Gene Product
Arabidopsis thaliana AT4G24050   NAD(P)-binding Rossmann-fold superfamily protein
Drosophila melanogaster Dmel_CG7675   CG7675 gene product from transcript CG7675-RC
Leishmania braziliensis LbrM.34.2100   hypothetical protein, conserved
Leishmania donovani LdBPK_352210.1   short chain dehydrogenase, putative
Leishmania infantum LinJ.35.2210   hypothetical protein, conserved
Leishmania major LmjF.35.2170   hypothetical protein, conserved
Leishmania mexicana LmxM.34.2170   hypothetical protein, conserved
Oryza sativa 4339991   Os06g0129100
Oryza sativa 4331397   Os03g0115700
Trypanosoma brucei gambiense Tbg972.9.8760   short-chain dehydrogenase, putative
Trypanosoma brucei Tb927.9.14040   short-chain dehydrogenase, putative
Trypanosoma cruzi TcCLB.508413.20   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.510757.20   hypothetical protein, conserved

Essentiality

Tb927.9.14040 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.4570 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.211.4570 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb09.211.4570 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.211.4570 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • 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
  • 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.

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) normal (PATO:0000461) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) normal (PATO:0000461) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in procyclic forms . References: 21363968
cell proliferation (GO:0008283) decreased (PATO:0000468) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: decreased cell proliferation (significant loss of fitness) in differentiation of procyclic to bloodstream forms . References: 21363968

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): 0.1


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 26.2% 130 aa Compounds References

Obtained from network model

Ranking Plot


Putative Drugs List


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

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

1 literature reference was collected for this gene.

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User comments

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Gene identifier Tb927.9.14040 (Trypanosoma brucei), short-chain dehydrogenase, putative
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