Detailed view for TcCLB.506635.80

Basic information

TDR Targets ID: 44473
Trypanosoma cruzi, Hydroxymethylglutaryl-CoA lyase, mitochondrial, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.3163 | Length (AA): 428 | MW (Da): 47051 | Paralog Number: 2

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

Druggability Group : DG1

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

PF00682   HMGL-like

Gene Ontology

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

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
4 423 1sr9 (A) 65 513 14.00 0 1 0.88 0.04
11 309 1ydn (A) 5 279 32.00 0 1 1.17 -1.51
8 313 2ftp (A) 4 285 32.00 0 1 1.08965 -0.55
9 311 1ydn (A) 3 281 32.00 0 1 1.04864 -0.21
9 419 5ks8 (D) 2 365 16.00 0.00000000073 1 1.00598 0.54
315 396 1wlz (A) 230 306 14.00 0 0.28 0.354189 -0.77

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 80-100% percentile metacyclic. Smircich P
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile epimastigote. Smircich P
Show/Hide expression data references
  • Smircich P Ribosome profiling reveals translation control as a key mechanism generating differential gene expression in Trypanosoma cruzi.

Orthologs

Ortholog group members (OG5_128474)

Species Accession Gene Product
Arabidopsis thaliana AT2G26800   Hydroxymethylglutaryl-CoA lyase
Caenorhabditis elegans CELE_Y71G12B.10   Protein Y71G12B.10
Dictyostelium discoideum DDB_G0283813   hydroxymethylglutaryl-CoA lyase
Drosophila melanogaster Dmel_CG10399   CG10399 gene product from transcript CG10399-RB
Homo sapiens ENSG00000146151   3-hydroxymethyl-3-methylglutaryl-CoA lyase-like 1
Homo sapiens ENSG00000117305   3-hydroxymethyl-3-methylglutaryl-CoA lyase
Mus musculus ENSMUSG00000007908   3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1
Mus musculus ENSMUSG00000028672   3-hydroxy-3-methylglutaryl-Coenzyme A lyase
Mycobacterium ulcerans MUL_2447   hypothetical protein
Neospora caninum NCLIV_020790   Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4), related
Oryza sativa 4349718   Os11g0137200
Oryza sativa 4326266   Os01g0269000
Oryza sativa 4351434   Os12g0134000
Schistosoma mansoni Smp_185140   hydroxymethylglutaryl-CoA lyase mitochondrial precursor
Schmidtea mediterranea mk4.030480.00   3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic
Schmidtea mediterranea mk4.005979.00   3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic
Schmidtea mediterranea mk4.006656.00  
Trypanosoma brucei gambiense Tbg972.4.2670   hydroxymethylglutaryl-CoA lyase, putative,3- hydroxy-3-methylglutarate-CoA lyase, putative
Trypanosoma brucei Tb927.4.2700   Hydroxymethylglutaryl-CoA lyase, mitochondrial, putative
Trypanosoma congolense TcIL3000_4_2580   Hydroxymethylglutaryl-CoA lyase, mitochondrial, putative
Trypanosoma cruzi TcCLB.508029.10   Hydroxymethylglutaryl-CoA lyase, mitochondrial, putative
Trypanosoma cruzi TcCLB.506635.80   Hydroxymethylglutaryl-CoA lyase, mitochondrial, putative
Trypanosoma cruzi TcCLB.508027.129   Hydroxymethylglutaryl-CoA lyase, mitochondrial, putative
Toxoplasma gondii TGME49_204460   hydroxymethylglutaryl-CoA lyase, putative

Essentiality

TcCLB.506635.80 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.2700 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.2700 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.4.2700 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.4.2700 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y71G12B.10 Caenorhabditis elegans embryonic lethal wormbase
TGME49_204460 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • 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
  • 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.
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

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

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
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

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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Gene identifier TcCLB.506635.80 (Trypanosoma cruzi), Hydroxymethylglutaryl-CoA lyase, mitochondrial, putative
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