Detailed view for Tb927.11.13730

Basic information

TDR Targets ID: 20293
Trypanosoma brucei, ornithine decarboxylase

Source Database / ID:  TriTrypDB  GeneDB

pI: 5.4633 | Length (AA): 423 | MW (Da): 46882 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0

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

PF00278   Pyridoxal-dependent decarboxylase, C-terminal sheet domain
PF02784   Pyridoxal-dependent decarboxylase, pyridoxal binding domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005575   cellular_component  
GO:0004586   ornithine decarboxylase activity  
GO:0003824   catalytic activity  
GO:0006596   polyamine biosynthetic process  

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
34 442 1f3t (A) 14 422 99.99 0 1 2.0357 -1.03

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:

  • 1F3T:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 1NJJ:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 1QU4:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 1SZR:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 2TOD:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% 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_126750)

Species Accession Gene Product
Arabidopsis thaliana AT3G14390   diaminopimelate decarboxylase 1
Arabidopsis thaliana AT5G11880   diaminopimelate decarboxylase 2
Brugia malayi Bm1_56455   Pyridoxal-dependent decarboxylase, pyridoxal binding domain containing protein
Candida albicans CaO19.6032   Ornithine decarboxylase similar to S. cerevisiae SPE1 (YKL184W) involved in pantothenate and polyamine biosynthesis
Candida albicans CaO19.13453   Ornithine decarboxylase similar to S. cerevisiae SPE1 (YKL184W) involved in pantothenate and polyamine biosynthesis
Caenorhabditis elegans CELE_K11C4.4   Protein ODC-1
Dictyostelium discoideum DDB_G0281109   Orn/DAP/Arg decarboxylase 2 domain-containing protein
Dictyostelium discoideum DDB_G0269856   Orn/DAP/Arg decarboxylase 2 domain-containing protein
Drosophila melanogaster Dmel_CG8719   Ornithine decarboxylase 2
Drosophila melanogaster Dmel_CG8721   Ornithine decarboxylase 1
Escherichia coli b2838   diaminopimelate decarboxylase, PLP-binding
Entamoeba histolytica EHI_100430   ornithine decarboxylase, putative
Giardia lamblia GL50803_94582   Ornithine decarboxylase
Homo sapiens ENSG00000115758   ornithine decarboxylase 1
Leishmania braziliensis LbrM.12.0300   ornithine decarboxylase, putative
Leishmania donovani LdBPK_120105.1   ornithine decarboxylase, putative
Leishmania infantum LinJ.12.0100   ornithine decarboxylase, putative
Leishmania major LmjF.12.0280   ornithine decarboxylase, putative
Leishmania mexicana LmxM.12.0280   ornithine decarboxylase, putative
Loa Loa (eye worm) LOAG_07980   pyridoxal-dependent decarboxylase
Mycobacterium leprae ML1128   PROBABLE DIAMINOPIMELATE DECARBOXYLASE LYSA (DAP DECARBOXYLASE)
Mus musculus ENSMUSG00000023120   predicted gene 853
Mus musculus ENSMUSG00000011179   ornithine decarboxylase, structural 1
Mycobacterium tuberculosis Rv1293   Diaminopimelate decarboxylase LysA (DAP decarboxylase)
Mycobacterium ulcerans MUL_3971   diaminopimelate decarboxylase LysA
Neospora caninum NCLIV_067260   Diaminopimelate decarboxylase protein, related
Oryza sativa 4329234   Os02g0440000
Oryza sativa 4347746   Os09g0543400
Oryza sativa 4335010   Os04g0136500
Onchocerca volvulus OVOC1740  
Plasmodium berghei PBANKA_0516900   S-adenosylmethionine decarboxylase/ornithine decarboxylase, putative
Plasmodium falciparum PF3D7_1033100   S-adenosylmethionine decarboxylase/ornithine decarboxylase
Plasmodium knowlesi PKNH_0617900   S-adenosylmethionine decarboxylase/ornithine decarboxylase, putative
Plasmodium vivax PVX_111070   S-adenosylmethionine decarboxylase-ornithine decarboxylase, putative
Plasmodium yoelii PY04754   S-adenosylmethionine decarboxylase-ornithine decarboxylase-related
Saccharomyces cerevisiae YKL184W   ornithine decarboxylase SPE1
Schmidtea mediterranea mk4.013057.00  
Schmidtea mediterranea mk4.012821.00  
Schmidtea mediterranea mk4.008099.00  
Schmidtea mediterranea mk4.023368.00  
Schmidtea mediterranea mk4.025019.00  
Schmidtea mediterranea mk4.007677.03  
Schmidtea mediterranea mk4.001750.03   Ornithine decarboxylase-1
Schmidtea mediterranea mk4.000699.03  
Schmidtea mediterranea mk4.014212.00  
Schmidtea mediterranea mk4.005186.01  
Schmidtea mediterranea mk4.021206.00  
Schmidtea mediterranea mk4.016468.00  
Schmidtea mediterranea mk4.022984.00  
Schmidtea mediterranea mk4.008099.01  
Schmidtea mediterranea mk4.008445.00  
Schmidtea mediterranea mk4.000260.08  
Schmidtea mediterranea mk4.009657.00  
Schmidtea mediterranea mk4.003300.00  
Trypanosoma brucei gambiense Tbg972.11.15320   ornithine decarboxylase, putative
Trypanosoma brucei Tb927.11.13730   ornithine decarboxylase
Trypanosoma congolense TcIL3000_0_32090   ornithine decarboxylase
Trypanosoma congolense TcIL3000.11.14030   ornithine decarboxylase, putative
Toxoplasma gondii TGME49_278740   diaminopimelate decarboxylase
Trichomonas vaginalis TVAG_001640   pyridoxal-dependent decarboxylase, putative
Trichomonas vaginalis TVAG_258030   ornithine decarboxylase, putative
Trichomonas vaginalis TVAG_205840   ornithine decarboxylase, putative
Trichomonas vaginalis TVAG_351660   diaminopimelate decarboxylase, putative
Trichomonas vaginalis TVAG_257110   diaminopimelate decarboxylase, putative
Trichomonas vaginalis TVAG_372420   conserved hypothetical protein

Essentiality

Tb927.11.13730 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.5300 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.01.5300 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.5300 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.5300 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b2838 Escherichia coli non-essential goodall
PBANKA_0516900 Plasmodium berghei Essential plasmo
TGME49_278740 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
growth (GO:0040007) lethal (sensu genetics) (PATO:0000718) single cell organism (CARO:0000064) bloodstream stage (PLO:0040) inferred from loss-of-function mutant phenotype (ECO:0000016) Trypanosoma brucei brucei No drug identifiers listed for this gene.
Annotator: ts4@sanger.ac.uk. Comment: . References: 9562432
growth (GO:0040007) lethal (sensu genetics) (PATO:0000718) single cell organism (CARO:0000064) bloodstream stage (PLO:0040) inferred from bioassay (ECO:0000094) Trypanosoma brucei brucei No drug identifiers listed for this gene.
Annotator: ts4@sanger.ac.uk. Comment: Drug: DFMO. . References: 11118342
growth (GO:0040007) lethal (sensu genetics) (PATO:0000718) single cell organism (CARO:0000064) bloodstream stage (PLO:0040) clinically validated (TDR:00010) Trypanosoma brucei gambiense No drug identifiers listed for this gene.
Annotator: ts4@sanger.ac.uk. Comment: Drug: DFMO. . References: 17128358
cell proliferation (GO:0008283) decreased (PATO:0000468) 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: decreased cell proliferation (significant loss 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): 1


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
Plasmodium falciparum S-adenosylmethionine decarboxylase/ornithine decarboxylase Compounds References
Rattus norvegicus Ornithine decarboxylase Compounds References
Homo sapiens ornithine decarboxylase 1 Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets

Obtained from network model

Ranking Plot


Putative Drugs List


Compound Raw Global Species
0.0239 0.7899 1
0.0243 0.3361 1
0.0234 0.6627 1
0.0246 0.323 1
0.0249 0.6563 1
0.0107 0.3813 1
0.0146 0.2911 0.453
0.0072 0.7179 0.5
0.021 0.2799 1
0.0124 0.3742 1
0.012 0.4486 1
0.0137 1 0.5
0.0058 0.3312 1
0.0098 0.2644 1
0.0158 0.3099 1
0.0072 1 0.5
0.0139 0.3288 0.5
0.0246 0.8245 1
0.0122 0.3743 1
0.0252 0.6408 1
0.0058 0.3145 1
0.0128 0.8693 0.5
0.0243 0.6443 1
0.0177 0.5524 1
0.0123 0.3784 1
0.0139 1 0.5
0.0134 0.4217 1
0.0066 1 1
0.0066 0.376 1
0.0245 0.3375 1
0.0243 0.3361 1
0.0122 0.3144 1
0.0155 1 0.5
0.0124 0.3742 1
0.004073 0.412894 1
0.0177 0.4839 1
0.0152 0.3064 1
0.0247 0.6468 1
0.0059 0.4269 1
0.0098 0.2667 1
0.0244 0.7029 1
0.0127 0.6172 0
0.0072 0.7179 0.5
0.0213 0.2849 1
0.0235 0.6445 1
0.0264 0.3859 1
0.0242 0.6684 1
0.0258 0.2869 1
0.0201 0.5072 1
0.0259 0.7094 1
0.0242 0.6684 1
0.006 0.387 0.5
0.0122 0.2673 1
0.0059 0.4269 1
0.0201 1 1
0.0147 1 1
0.0129 0.4371 1
0.0205 1 1
0.0102 0.8506 1
0.0161 0.4267 1
0.0117 0.326 0.5
0.0135 1 0.5
0.0242 0.6684 1
0.0139 0.6024 1
0.0058 0.3871 1
0.0248 0.2629 1
0.024 0.7295 0.5
0.012 0.2832 1
0.0248 0.2629 1
0.0059 0.4269 1
0.0175 0.491 0.5

Assayability

Assay information

  • BRENDA Assay
  • An enzyme with this EC number or name or sequence has been assayed in Trypanosoma brucei ( 6 )

Reagent availability

  • Reagent:
  • Target Type Source Notes
    Tb927.11.13730 purified protein BRENDA A protein with this EC number or name or sequence has been purified from Trypanosoma brucei ( 6 )

Bibliographic References

11 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

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier Tb927.11.13730 (Trypanosoma brucei), ornithine decarboxylase
Title for this comment
Comment