Detailed view for TGME49_278740

Basic information

TDR Targets ID: 259655
Toxoplasma gondii, diaminopimelate decarboxylase
Source Database / ID:  ToxoDB 

pI: 6.8182 | Length (AA): 686 | MW (Da): 75668 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 1

Druggability Group : DG5

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:0008836   diaminopimelate decarboxylase activity  
GO:0003824   catalytic activity  
GO:0009089   lysine biosynthetic process via diaminopimelate  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
3 459 1twi (A) 33 441 27.00 0 1 1.11 -0.37
13 445 1knw (A) 2 397 28.00 0 1 1.17 -0.36
55 287 1ct5 (A) 9 244 11.00 0 0.55 0.41 -0.42
104 593 2o0t (A) 8 445 25.00 0 1 0.804186 0.49
127 593 2yxx (A) 4 384 35.00 0 1 0.830658 0.59
134 595 2qgh (A) 11 400 36.00 0 1 0.835069 0.51

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
Mid 40-60% percentile ME49 merozoite. Hehl AB
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile VEG Tachyzoite, ME49 Tachyzoite, ME49 Oocyst, ME49 Bradyzoite. Gregory Fritz HM Sibley/Greg
Show/Hide expression data references
  • Sibley/Greg ToxoDB
  • Fritz HM Transcriptomic analysis of toxoplasma development reveals many novel functions and structures specific to sporozoites and oocysts.
  • Gregory ToxoDB
  • Hehl AB Asexual expansion of Toxoplasma gondii merozoites is distinct from tachyzoites and entails expression of non-overlapping gene families to attach, invade, and replicate within feline enterocytes.

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

TGME49_278740 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.5300 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.01.5300 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.5300 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.5300 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 this record Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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
  • 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.
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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)

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): 0.5

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

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier TGME49_278740 (Toxoplasma gondii), diaminopimelate decarboxylase
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