Detailed view for EHI_095890

Basic information

TDR Targets ID: 802011
Entamoeba histolytica, DNA-directed RNA polymerase I largest subunit, putative
Source Database / ID:  AmoebaDB  

pI: 6.7538 | Length (AA): 1570 | MW (Da): 178069 | Paralog Number: 0

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

Druggability Group : DG2

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

PF00623   RNA polymerase Rpb1, domain 2
PF04983   RNA polymerase Rpb1, domain 3
PF04997   RNA polymerase Rpb1, domain 1
PF04998   RNA polymerase Rpb1, domain 5
PF05000   RNA polymerase Rpb1, domain 4

Gene Ontology

Mouse over links to read term descriptions.
GO:0006351   transcription, DNA-dependent  
GO:0005634   nucleus  
GO:0008270   zinc ion binding  
GO:0003899   DNA-directed RNA polymerase activity  
GO:0003677   DNA binding  

Metabolic Pathways

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

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
2 1566 3h0g (A) 9 1452 30.00 0 1 0.908715 1.95
16 1567 4c3i (A) 10 1660 37.00 0 1 1.28193 0.55
16 1567 4c3i (A) 10 1660 40.00 0 1 1.20443 0.71
1286 1375 4uos (A) 3 91 20.00 0 0.03 0.364725 -2.03
1286 1369 5wsu (C) 769 849 20.00 0 0 0.295903 -1.67

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 Trophozoite, Rahman HM-1 IMSS Trophozoite. Hon CC
Show/Hide expression data references
  • Hon CC Transcriptomics of virulent and avirulent strains

Orthologs

Ortholog group members (OG5_127924)

Species Accession Gene Product
Arabidopsis thaliana AT3G57660   nuclear RNA polymerase A1
Babesia bovis BBOV_IV009600   DNA directed RNA polymerase
Brugia malayi Bm1_43180   RNA polymerase Rpb1, domain 2 family protein
Candida albicans CaO19.1839   RNA polymerase I largest subunit
Candida albicans CaO19.9397   RNA polymerase I largest subunit
Caenorhabditis elegans CELE_Y48E1A.1   Protein RPOA-1, isoform B
Cryptosporidium hominis Chro.50318   DNA-directed RNA polymerase
Cryptosporidium parvum cgd5_730   DNA-directed RNA polymerase I, putative
Dictyostelium discoideum DDB_G0275759   RNA polymerase I, largest subunit
Drosophila melanogaster Dmel_CG10122   RNA polymerase I subunit
Echinococcus granulosus EgrG_001022100   DNA directed RNA polymerase I subunit RPA1
Entamoeba histolytica EHI_095890   DNA-directed RNA polymerase I largest subunit, putative
Echinococcus multilocularis EmuJ_001022100   DNA directed RNA polymerase I subunit RPA1
Giardia lamblia GL50803_23496   RNA polymerase AI large subunit
Homo sapiens ENSG00000068654   polymerase (RNA) I polypeptide A, 194kDa
Leishmania braziliensis LbrM.16.1400   DNA-directed rna polymerase I largest subunit, putative
Leishmania donovani LdBPK_161420.1   DNA-directed rna polymerase I largest subunit, putative
Leishmania infantum LinJ.16.1420   DNA-directed rna polymerase I largest subunit, putative
Leishmania major LmjF.16.1350   DNA-directed rna polymerase I largest subunit, putative
Leishmania mexicana LmxM.16.1350   DNA-directed rna polymerase I largest subunit, putative
Loa Loa (eye worm) LOAG_01639   hypothetical protein
Mus musculus ENSMUSG00000049553   polymerase (RNA) I polypeptide A
Neospora caninum NCLIV_019340   DNA-directed rna polymerase I largest subunit, putative
Oryza sativa 9270399   Os06g0612150
Plasmodium berghei PBANKA_1109000   RNA polymerase I, putative
Plasmodium falciparum PF3D7_0509400   RNA polymerase I
Plasmodium knowlesi PKNH_1024200   RNA polymerase I, putative
Plasmodium vivax PVX_098025   DNA-directed RNA polymerase I 190 kDa polypeptide, putative
Plasmodium yoelii PY03255   RNA polymerase A/beta'/A'' subunit, putative
Saccharomyces cerevisiae YOR341W   DNA-directed RNA polymerase I core subunit RPA190
Schistosoma japonicum Sjp_0090080   DNA-directed RNA polymerase I subunit RPA1, putative
Schistosoma japonicum Sjp_0090090   DNA-directed RNA polymerase I subunit RPA1, putative
Schistosoma japonicum Sjp_0090100   ko:K02999 DNA-directed RNA polymerase I subunit A1, putative
Schistosoma japonicum Sjp_0090070   DNA-directed RNA polymerase I subunit RPA1, putative
Schistosoma japonicum Sjp_0021430   DNA-directed RNA polymerase I subunit rpa1, putative
Schistosoma mansoni Smp_129500   DNA-directed RNA polymerase I
Schmidtea mediterranea mk4.000030.02   DNA-directed RNA polymerase I subunit RPA1
Schmidtea mediterranea mk4.000030.03  
Schmidtea mediterranea mk4.000030.00  
Trypanosoma brucei gambiense Tbg972.8.4910   DNA-directed rna polymerase I largest subunit, putative
Trypanosoma brucei Tb11.v5.0723   DNA-directed rna polymerase I largest subunit, putative
Trypanosoma brucei Tb927.8.5090   DNA-directed RNA polymerase I largest subunit
Trypanosoma congolense TcIL3000_8_4870   DNA-directed rna polymerase I largest subunit, putative
Trypanosoma cruzi TcCLB.511381.40   DNA-directed rna polymerase I largest subunit, putative
Toxoplasma gondii TGME49_244880   DNA-directed RNA polymerase I RPA1
Theileria parva TP01_0809   RNA polymerase large subunit, putative
Trichomonas vaginalis TVAG_591230   RNA polymerase A, putative

Essentiality

EHI_095890 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.5090 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.8.5090 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.8.5090 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.8.5090 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
YOR341W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1109000 Plasmodium berghei Essential plasmo
TGME49_244880 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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

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 polymerase (RNA) I polypeptide A, 194kDa 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
0.0191886 1 1
0.0061 0.2869 1
0.0018 1 1
0.003 0.3536 1
0.0092 1 1
0.00927523 1 1
0.0076 1 1
0.0211 0.4768 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.

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User comments

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Gene identifier EHI_095890 (Entamoeba histolytica), DNA-directed RNA polymerase I largest subunit, putative
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