Detailed view for TGME49_201700

Basic information

TDR Targets ID: 262533
Toxoplasma gondii, WD domain, G-beta repeat-containing protein
Source Database / ID:  ToxoDB 

pI: 7.4252 | Length (AA): 654 | MW (Da): 67437 | Paralog Number: 1

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

Druggability Group : DG3

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

PF00400   WD domain, G-beta repeat

Gene Ontology

Mouse over links to read term descriptions.
GO:1904263   GO:positive regulation of TORC1 signaling  

GO:0090114   GO:COPII-coated vesicle budding  

GO:0030127   COPII vesicle coat  
GO:0005515   protein binding  
GO:0005198   structural molecule activity  
GO:0016192   vesicle-mediated transport  

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
4 315 1p22 (A) 296 545 20.00 0 1 0.32 0.13
75 437 3fm0 (A) 20 321 33.00 0.000000000006 1 0.650146 0.14
109 357 2h9l (A) 22 216 30.00 0.00013 0.94 0.427834 0.56
403 528 2mqa (A) 18 138 11.00 0 0 0.266661 -0.92
492 539 2kpy (A) 57 106 46.00 0.15 0.02 0.426495 -0.32

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 VEG Tachyzoite, ME49 merozoite. Gregory Hehl AB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile ME49 Tachyzoite, ME49 Bradyzoite. Gregory Sibley/Greg
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile ME49 Oocyst. Fritz HM
Show/Hide expression data references
  • 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.
  • Gregory ToxoDB
  • Fritz HM Transcriptomic analysis of toxoplasma development reveals many novel functions and structures specific to sporozoites and oocysts.

Orthologs

Ortholog group members (OG5_127687)

Species Accession Gene Product
Arabidopsis thaliana AT3G01340   transport protein SEC13B
Arabidopsis thaliana AT2G30050   transport protein SEC13A
Brugia malayi Bm1_36835   SEC13-related protein
Candida albicans CaO19.7948   WD domain protein similar to S. cerevisiae SEC13 (YLR208W) secretory pathway vesicle COPII coat component
Candida albicans CaO19.316   WD domain protein similar to S. cerevisiae SEC13 (YLR208W) secretory pathway vesicle COPII coat component
Caenorhabditis elegans CELE_Y77E11A.13   Protein NPP-20, isoform B
Cryptosporidium hominis Chro.80472   hypothetical protein
Cryptosporidium parvum cgd8_4110   hypothetical protein
Dictyostelium discoideum DDB_G0292052   WD40 repeat-containing protein
Drosophila melanogaster Dmel_CG6773   Sec13 ortholog (S. cerevisiae)
Echinococcus granulosus EgrG_000149000   sec13 protein
Entamoeba histolytica EHI_001050   sec 13 protein, putative
Echinococcus multilocularis EmuJ_000149000   sec13 protein
Giardia lamblia GL50803_137698   Sec13
Homo sapiens ENSG00000157020   SEC13 homolog (S. cerevisiae)
Leishmania braziliensis LbrM.32.0100   protein transport protein Sec13, putative
Leishmania donovani LdBPK_320050.1   protein transport protein SEC13
Leishmania infantum LinJ.32.0050   protein transport protein Sec13, putative
Leishmania major LmjF.32.0050   protein transport protein Sec13, putative
Leishmania mexicana LmxM.31.0050   protein transport protein Sec13, putative
Loa Loa (eye worm) LOAG_01167   Sec13l1-prov protein
Mus musculus ENSMUSG00000030298   SEC13 homolog (S. cerevisiae)
Neospora caninum NCLIV_023040   hypothetical protein
Oryza sativa 4334673   Os03g0831800
Oryza sativa 4342827   Os07g0246300
Oryza sativa 4328228   Os02g0135800
Plasmodium berghei PBANKA_1445400   protein transport protein SEC13, putative
Plasmodium falciparum PF3D7_1230700   protein transport protein SEC13
Plasmodium knowlesi PKNH_1450100   protein transport protein SEC13, putative
Plasmodium vivax PVX_124175   protein transport protein SEC13, putative
Plasmodium yoelii PY01574   hypothetical protein
Plasmodium yoelii PY03775   hypothetical protein
Saccharomyces cerevisiae YLR208W   GTPase-activating protein SEC13
Schistosoma japonicum Sjp_0010270   ko:K08171 MFS transporter, OPA family, solute carrier family 37, putative
Schistosoma japonicum Sjp_0302910   Protein SEC13 homolog, putative
Schistosoma mansoni Smp_090870   protein transport protein Sec13
Schmidtea mediterranea mk4.007775.04   Protein SEC13 homolog
Schmidtea mediterranea mk4.002474.03   Protein SEC13 homolog
Trypanosoma brucei gambiense Tbg972.10.16570   protein transport protein Sec13, putative
Trypanosoma brucei Tb927.10.14180   protein transport protein SEC13
Trypanosoma congolense TcIL3000_10_12050   protein transport protein SEC13
Trypanosoma cruzi TcCLB.506525.20   protein transport protein SEC13
Trypanosoma cruzi TcCLB.511283.20   protein transport protein SEC13
Toxoplasma gondii TGME49_201700   WD domain, G-beta repeat-containing protein
Toxoplasma gondii TGME49_201690   BT1 family protein
Trichomonas vaginalis TVAG_456890   protein transport protein sec13, putative
Trichomonas vaginalis TVAG_158010   protein transport protein SEC13, putative

Essentiality

TGME49_201700 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.14180 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.10.14180 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.14180 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.10.14180 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y77E11A.13 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y77E11A.13 Caenorhabditis elegans larval arrest wormbase
CELE_Y77E11A.13 Caenorhabditis elegans larval lethal wormbase
CELE_Y77E11A.13 Caenorhabditis elegans slow growth wormbase
CELE_Y77E11A.13 Caenorhabditis elegans sterile wormbase
YLR208W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1445400 Plasmodium berghei Essential plasmo
TGME49_201690 Toxoplasma gondii Essentiality uncertain sidik
TGME49_201700 this record Toxoplasma gondii Essentiality uncertain sidik
TGME49_201690 Toxoplasma gondii Probably essential sidik
TGME49_201700 this record Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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
  • 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.
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

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
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 TGME49_201700 (Toxoplasma gondii), WD domain, G-beta repeat-containing protein
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