Detailed view for EHI_040320

Basic information

TDR Targets ID: 798558
Entamoeba histolytica, 3 exoribonuclease family protein
Source Database / ID:  AmoebaDB  

pI: 4.9272 | Length (AA): 238 | MW (Da): 26602 | 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

PF01138   3' exoribonuclease family, domain 1
PF03725   3' exoribonuclease family, domain 2

Gene Ontology

Mouse over links to read term descriptions.
No GO information for this protein.

Metabolic Pathways

RNA degradation (KEGG)

Structural information

Modbase 3D models:

There are 3 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
1 237 3u1k (A) 349 605 20.00 0 1 1.1509 0.22
3 235 2po1 (A) 10 244 34.00 0 1 1.46209 -0.62
4 231 2nn6 (B) 6 237 39.00 0 1 1.42418 -0.06

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 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_127234)

Species Accession Gene Product
Arabidopsis thaliana AT3G61620   exonuclease RRP41
Babesia bovis BBOV_IV005940   exosome complex exonuclease rrp41, putative
Brugia malayi Bm1_33890   Putative exosome complex exonuclease RRP41
Candida albicans CaO19.12051   likely 3' exoribonuclease similar to S. cerevisiae SKI6 (YGR195W)exosome component involved mRNA degradation and nuclear RNA pro
Candida albicans CaO19.4582   likely 3' exoribonuclease similar to S. cerevisiae SKI6 (YGR195W)exosome component involved mRNA degradation and nuclear RNA pro
Caenorhabditis elegans exos-4.1   Protein EXOS-4.1, isoform A
Cryptosporidium hominis Chro.40450   exosome complex exonuclease RRP41
Cryptosporidium parvum cgd4_3930   archeo-eukaryotic exosomal RNAse
Dictyostelium discoideum DDB_G0291328   hypothetical protein
Drosophila melanogaster Dmel_CG15481   CG15481 gene product from transcript CG15481-RB
Echinococcus granulosus EgrG_000458000   exosome complex component RRP41
Entamoeba histolytica EHI_040320   3 exoribonuclease family protein
Echinococcus multilocularis EmuJ_000458000   exosome complex component RRP41
Homo sapiens ENSG00000178896   exosome component 4
Leishmania braziliensis LbrM.35.3240   exosome complex exonuclease rrp41, putative
Leishmania donovani LdBPK_363170.1   Ribosomal RNA processing protein 41A
Leishmania infantum LinJ.36.3170   exosome complex exonuclease rrp41, putative
Leishmania major LmjF.36.3020   exosome complex exonuclease rrp41, putative
Leishmania mexicana LmxM.36.3020   exosome complex exonuclease rrp41, putative
Loa Loa (eye worm) LOAG_00358   EXOSome component family member
Mycobacterium leprae ML1174   PROBABLE RIBONUCLEASE RPHA (RNase PH) (tRNA nucleotidyltransferase)
Mus musculus ENSMUSG00000034259   exosome component 4
Mycobacterium tuberculosis Rv1340   Probable ribonuclease RphA (RNase PH) (tRNA nucleotidyltransferase)
Mycobacterium ulcerans MUL_3908   ribonuclease PH
Neospora caninum NCLIV_031410   hypothetical protein
Oryza sativa 4346519   Os09g0252000
Onchocerca volvulus OVOC2627   Mitochondrial import inner membrane translocase subunit Tim10B homolog
Plasmodium berghei PBANKA_1016800   exosome complex exonuclease RRP41, putative
Plasmodium falciparum PF3D7_1427800   exosome complex exonuclease RRP41, putative
Plasmodium knowlesi PKNH_1330900   exosome complex exonuclease RRP41, putative
Plasmodium vivax PVX_085150   exosome complex exonuclease RRP41, putative
Plasmodium yoelii PY07159   exonuclease RRP41, putative
Saccharomyces cerevisiae YGR195W   Ski6p
Schistosoma japonicum Sjp_0304560   ko:K01149 Ski6 [EC:3.1.13.-], putative
Schistosoma mansoni Smp_012110   ribonuclease pH related
Schmidtea mediterranea mk4.009255.04   Exosome complex component RRP41
Schmidtea mediterranea mk4.000566.05   Exosome complex component RRP41
Schmidtea mediterranea mk4.000940.04   Exosome complex component RRP41
Schmidtea mediterranea mk4.023580.00   Exosome complex component RRP41
Schmidtea mediterranea mk4.014029.02   Exosome complex component RRP41
Schmidtea mediterranea mk4.034062.01  
Schmidtea mediterranea mk4.006882.02   Exosome complex component RRP41
Schmidtea mediterranea mk4.008988.01   Exosome complex component RRP41
Trypanosoma brucei gambiense Tbg972.10.9130   exosome complex exonuclease RRP41A,RRP41p homologue, putative
Trypanosoma brucei Tb927.10.7450   Ribosomal RNA processing protein 41A
Trypanosoma congolense TcIL3000_10_6420   Ribosomal RNA processing protein 41A
Trypanosoma cruzi TcCLB.509715.9   Ribosomal RNA processing protein 41A
Trypanosoma cruzi TcCLB.510105.20   exosome complex exonuclease RRP41A
Theileria parva TP01_0398   exosome complex exonuclease rrp41, putative
Trichomonas vaginalis TVAG_250040   Exosome complex exonuclease RRP41, putative

Essentiality

EHI_040320 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.7450 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.10.7450 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.7450 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.10.7450 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
YGR195W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1016800 Plasmodium berghei Slow plasmo
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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

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 EHI_040320 (Entamoeba histolytica), 3 exoribonuclease family protein
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