Detailed view for TGME49_258240

Basic information

TDR Targets ID: 260190
Toxoplasma gondii, chromodomain helicase DNA binding protein CHD1/SWI2/SNF2
Source Database / ID:  ToxoDB 

pI: 6.5766 | Length (AA): 2492 | MW (Da): 271394 | Paralog Number: 0

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

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

PF00176   SNF2 family N-terminal domain
PF00271   Helicase conserved C-terminal domain
PF00385   Chromo (CHRromatin Organisation MOdifier) domain
PF13907   Domain of unknown function (DUF4208)

Gene Ontology

Mouse over links to read term descriptions.
GO:0005634   nucleus  
GO:0000785   chromatin  
GO:0005524   ATP binding  
GO:0004386   helicase activity  
GO:0003682   chromatin binding  
GO:0003677   DNA binding  
GO:0003676   nucleic acid binding  
GO:0043044   ATP-dependent chromatin remodeling  
GO:0006333   chromatin assembly or disassembly  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 10 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
900 1546 1z3i (X) 95 735 25.00 0 1 0.12 -0.22
1271 1429 1fuk (A) 235 385 18.00 0.000000000077 1 0.35 -1.13
6 59 2kpy (A) 56 108 26.00 0.058 0 0.288369 -0.37
173 292 2mqa (A) 20 138 10.00 0 0.02 0.125754 -0.35
484 524 4x8w (H) 1 209 51.00 0.41 0.06 0.214553 3.08
628 812 4o42 (A) 270 439 28.00 0 0.94 0.226238 0.41
692 1520 3mwy (W) 212 914 43.00 0 1 0.432765 1.2
958 1430 1z3i (X) 145 640 36.00 0 1 0.550907 -0.21
1271 1423 2hjv (A) 216 363 22.00 0 1 0.394396 -0.98
1964 2024 4b4c (A) 1253 1320 46.00 0.00022 0.68 0.286578 -0.44

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 VEG Tachyzoite, ME49 Tachyzoite. Gregory
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile ME49 Oocyst, ME49 Bradyzoite. Fritz HM Sibley/Greg
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile ME49 merozoite. Hehl AB
Show/Hide expression data references
  • Fritz HM Transcriptomic analysis of toxoplasma development reveals many novel functions and structures specific to sporozoites and oocysts.
  • Gregory ToxoDB
  • Sibley/Greg 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_128209)

Species Accession Gene Product
Arabidopsis thaliana AT2G13370   chromatin remodeling 5
Babesia bovis BBOV_IV009080   chromo-helicase DNA-binding protein, putative
Brugia malayi Bm1_28925   Type III restriction enzyme, res subunit family protein
Candida albicans CaO19.10553   transcriptional regulator
Candida albicans CaO19.3035   transcriptional regulator
Caenorhabditis elegans CELE_H06O01.2   Protein CHD-1
Cryptosporidium hominis Chro.10413   chromodomain-helicase-DNA-binding protein, CHD-1-related
Cryptosporidium parvum cgd1_3670   CHD3 ortholog with 2x chromodomains plus SNF2 ATpase (2chromo+helicase+Znf_NFX)
Dictyostelium discoideum DDB_G0284171   CHR group protein
Drosophila melanogaster Dmel_CG3733   Chromodomain-helicase-DNA-binding protein 1
Echinococcus granulosus EgrG_000760900   chromodomain helicase DNA binding protein 1
Entamoeba histolytica EHI_141900   chromodomain-helicase-DNA-binding protein, putative
Echinococcus multilocularis EmuJ_000760900   chromodomain helicase DNA binding protein 1
Giardia lamblia GL50803_112978   Chromodomain helicase-DNA-binding protein, putative
Homo sapiens ENSG00000173575   chromodomain helicase DNA binding protein 2
Homo sapiens ENSG00000153922   chromodomain helicase DNA binding protein 1
Loa Loa (eye worm) LOAG_04448   hypothetical protein
Mus musculus ENSMUSG00000078671   chromodomain helicase DNA binding protein 2
Mus musculus ENSMUSG00000023852   chromodomain helicase DNA binding protein 1
Neospora caninum NCLIV_028160   hypothetical protein
Oryza sativa 4344175   Os07g0660200
Plasmodium berghei PBANKA_0508100   chromodomain-helicase-DNA-binding protein 1, putative
Plasmodium falciparum PF3D7_1023900   chromodomain-helicase-DNA-binding protein 1 homolog, putative
Plasmodium knowlesi PKNH_0608400   chromodomain-helicase-DNA-binding protein 1 homolog, putative
Plasmodium vivax PVX_111520   hypothetical protein, conserved
Plasmodium yoelii PY02297   chromodomain-helicase-DNA-binding protein, CHD-1-related
Saccharomyces cerevisiae YER164W   chromatin-remodeling ATPase CHD1
Schistosoma japonicum Sjp_0000710   ko:K01509 adenosinetriphosphatase [EC3.6.1.3], putative
Schistosoma mansoni Smp_041760   chromodomain helicase DNA binding protein
Schmidtea mediterranea mk4.003381.01   Putative chromodomain helicase DNA binding protein
Schmidtea mediterranea mk4.014198.00   Putative chromodomain helicase DNA binding protein
Toxoplasma gondii TGME49_258240   chromodomain helicase DNA binding protein CHD1/SWI2/SNF2
Theileria parva TP01_0866   hypothetical protein

Essentiality

TGME49_258240 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
PBANKA_0508100 Plasmodium berghei Essential plasmo
TGME49_258240 this record Toxoplasma gondii Essentiality uncertain 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
  • 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
  • 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
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • 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)

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.

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

User comments

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Gene identifier TGME49_258240 (Toxoplasma gondii), chromodomain helicase DNA binding protein CHD1/SWI2/SNF2
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