Detailed view for TGME49_233720

Basic information

TDR Targets ID: 262611
Toxoplasma gondii, DNA-directed RNA polymerase II RPBABC8
Source Database / ID:  ToxoDB 

pI: 5.3072 | Length (AA): 149 | MW (Da): 17057 | Paralog Number: 0

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

PF03870   RNA polymerase Rpb8

Gene Ontology

Mouse over links to read term descriptions.
GO:0006351   transcription, DNA-dependent  
GO:0006350   transcription  

Metabolic Pathways

Purine metabolism (KEGG)
Pyrimidine metabolism (KEGG)
Global map (KEGG)
RNA polymerase (KEGG)

Structural information

Modbase 3D models:

There are 4 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
3 140 1twf (H) 2 146 37.00 0 1 1.31 -0.38
2 140 3h0g (H) 2 125 41.00 0 0.86 1.22289 0.61
3 140 3cqz (H) 2 146 41.00 0 1 1.13537 0.13
5 140 3gtj (H) 4 146 36.00 0 0.95 1.27975 0.25

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 Oocyst, ME49 Bradyzoite. Gregory Fritz HM Sibley/Greg
Show/Hide expression data references
  • Gregory ToxoDB
  • Fritz HM Transcriptomic analysis of toxoplasma development reveals many novel functions and structures specific to sporozoites and oocysts.
  • 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.
  • Sibley/Greg ToxoDB

Orthologs

Ortholog group members (OG5_127936)

Species Accession Gene Product
Arabidopsis thaliana AT3G59600   RNA polymerase Rpb8
Arabidopsis thaliana AT1G54250   DNA-directed RNA polymerases II and V subunit 8A
Babesia bovis BBOV_IV005100   RNA polymerase subunit 8c, putative
Brugia malayi Bm1_26995   DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide
Candida albicans CaO19.6314   16-kDa RNA polymerase subunit
Candida albicans CaO19.13691   16-kDa RNA polymerase subunit
Caenorhabditis elegans CELE_F26F4.11   Protein RPB-8
Cryptosporidium hominis Chro.10257   RNA polymerase subunit 8c
Cryptosporidium parvum cgd1_2260   RNA polymerase II B8 subunit
Dictyostelium discoideum DDB_G0278039   RNA polymerase I core subunit
Drosophila melanogaster Dmel_CG11246   CG11246 gene product from transcript CG11246-RA
Echinococcus granulosus EgrG_000117600   dna directed rna polymerases i ii and iii
Entamoeba histolytica EHI_038570   RNA polymerase subunit Rpb8
Echinococcus multilocularis EmuJ_000117600   dna directed rna polymerases i ii and iii
Giardia lamblia GL50803_15144   RNA polymerase II subunit Rpb8
Homo sapiens ENSG00000163882   polymerase (RNA) II (DNA directed) polypeptide H
Leishmania braziliensis LbrM.28.0850   RNA polymerase B subunit RPB8, putative
Leishmania donovani LdBPK_280870.1   RNA polymerase B subunit RPB8, putative
Leishmania infantum LinJ.28.0870   RNA polymerase B subunit RPB8, putative
Leishmania major LmjF.28.0810   RNA polymerase B subunit RPB8, putative
Leishmania mexicana LmxM.28.0810   RNA polymerase B subunit RPB8, putative
Loa Loa (eye worm) LOAG_00799   DNA-directed RNA polymerase I
Mus musculus ENSMUSG00000021018   polymerase (RNA) II (DNA directed) polypeptide H
Mus musculus 102640226   DNA-directed RNA polymerases I, II, and III subunit RPABC3-like
Neospora caninum NCLIV_033350   UDP-glucose 4-epimerase Gal10, related
Oryza sativa 4341946   Os06g0697400
Oryza sativa 4334766   Os03g0845700
Plasmodium berghei PBANKA_1429500   DNA-directed RNA polymerases I, II, and III subunit RPABC3, putative
Plasmodium falciparum PF3D7_1213700   DNA-directed RNA polymerases I, II, and III subunit RPABC3, putative
Plasmodium knowlesi PKNH_1433200   DNA-directed RNA polymerases I, II, and III subunit RPABC3, putative
Plasmodium vivax PVX_123375   RNA polymerase subunit 8c, putative
Plasmodium yoelii PY02017   DNA-directed RNA polymerases i, ii, and iii 17.1 kDa polypeptide
Saccharomyces cerevisiae YOR224C   DNA-directed RNA polymerase core subunit RPB8
Schistosoma japonicum Sjp_0070380   ko:K03016 DNA-directed RNA polymerase II subunit H, putative
Schistosoma mansoni Smp_006850   DNA-directed rna polymerase subunit rpb8
Schmidtea mediterranea mk4.004862.04   Probable DNA-directed RNA polymerases I, II, and III subunit RPABC3
Schmidtea mediterranea mk4.007396.00   Probable DNA-directed RNA polymerases I, II, and III subunit RPABC3
Trypanosoma brucei gambiense Tbg972.11.9040   RNA polymerase B subunit RPB8, putative
Trypanosoma brucei Tb927.11.7930   RNA polymerase B subunit RPB8, putative
Trypanosoma cruzi TcCLB.506933.80   RNA polymerase B subunit RPB8, putative
Toxoplasma gondii TGME49_233720   DNA-directed RNA polymerase II RPBABC8
Theileria parva TP01_0233   RNA polymerase subunit, putative
Trichomonas vaginalis TVAG_186530   DNA-directed RNA polymerase subunit rpb8, putative

Essentiality

TGME49_233720 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.02.5790 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.02.5790 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.02.5790 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.02.5790 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F26F4.11 Caenorhabditis elegans embryonic lethal wormbase
CELE_F26F4.11 Caenorhabditis elegans larval arrest wormbase
CELE_F26F4.11 Caenorhabditis elegans slow growth wormbase
CELE_F26F4.11 Caenorhabditis elegans sterile wormbase
YOR224C Saccharomyces cerevisiae inviable yeastgenome
TGME49_233720 this record Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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

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

  • Assay for Ribonucleic Acid Polymerase (2.7.7.6 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

No reagent availability information for this target.

Bibliographic References

1 literature reference was collected for this gene.

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_233720 (Toxoplasma gondii), DNA-directed RNA polymerase II RPBABC8
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