Detailed view for TcCLB.503653.30

Basic information

TDR Targets ID: 34174
Trypanosoma cruzi, RNase PH-like protein, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.683 | Length (AA): 284 | MW (Da): 30404 | Paralog Number: 1

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

Gene Ontology

Mouse over links to read term descriptions.
GO:0000175   3'-5'-exoribonuclease activity  
GO:0003723   RNA binding  
GO:0006396   RNA processing  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 8 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
1 278 2br2 (B) 13 234 24.00 0 1 1 -0.14
4 252 2ba0 (F) 14 246 22.00 0 0.63 1.1 -0.07
7 160 2br2 (B) 19 166 31.00 0.00000000002 0.98 0.97 -0.7
5 256 3m7n (D) 15 250 23.00 0 0.97 1.12272 0.23
7 206 2nn6 (B) 12 206 32.00 0 1 0.988825 0.67
7 282 1r6l (A) 3 239 20.00 0 1 0.929231 0.54
11 250 2nn6 (F) 31 247 35.00 0.00000000022 0.98 0.86367 1.31
18 157 5jea (F) 45 193 21.00 0.056 1 0.624358 -0.3

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 epimastigote, metacyclic. Smircich P
Show/Hide expression data references
  • Smircich P Ribosome profiling reveals translation control as a key mechanism generating differential gene expression in Trypanosoma cruzi.

Orthologs

Ortholog group members (OG5_128693)

Species Accession Gene Product
Arabidopsis thaliana AT3G46210   ribosomal protein S5 domain 2-like superfamily protein
Brugia malayi Bm1_42620   DNA segment, Chr 7, Wayne State University 180, expressed
Candida albicans CaO19.81   similar to S. cerevisiae RRP46 (YGR095C) exosome component involved mRNA degradation and nuclear RNA processing
Caenorhabditis elegans CELE_C14A4.5   Protein CRN-5
Cryptosporidium hominis Chro.40220   hypothetical protein
Cryptosporidium parvum cgd4_1950   RPR46-like RNAse PH domain
Dictyostelium discoideum DDB_G0284053   hypothetical protein
Drosophila melanogaster Dmel_CG4043   CG4043 gene product from transcript CG4043-RA
Echinococcus granulosus EgrG_001137700   exosome complex exonuclease RRP46
Entamoeba histolytica EHI_086520   3 exoribonuclease family protein
Echinococcus multilocularis EmuJ_001137700   exosome complex exonuclease RRP46
Giardia lamblia GL50803_1890   3 exoribonuclease, putative
Homo sapiens ENSG00000077348   exosome component 5
Leishmania donovani LdBPK_020290.1   ribosomal RNA processing protein 41B, putative
Leishmania infantum LinJ.02.0290   ribosomal RNA processing protein, putative
Leishmania major LmjF.02.0320   ribosomal RNA processing protein, putative
Leishmania mexicana LmxM.02.0320   ribosomal RNA processing protein, putative
Loa Loa (eye worm) LOAG_03684   hypothetical protein
Mus musculus ENSMUSG00000061286   exosome component 5
Neospora caninum NCLIV_044790   3 exoribonuclease family, domain 1 containing protein, putative
Oryza sativa 4334824   Os03g0854200
Saccharomyces cerevisiae YGR095C   Rrp46p
Schistosoma japonicum Sjp_0028190   expressed protein
Schistosoma mansoni Smp_056900   ribonuclease pH related
Schmidtea mediterranea mk4.001849.03   Ribonuclease pH related
Trypanosoma brucei gambiense Tbg.972.2.740   ribosomal RNA processing protein 41B,RNase PH-like protein,exosome complex exonuclease 1
Trypanosoma brucei Tb927.2.2180   ribosomal RNA processing protein 41B
Trypanosoma congolense TcIL3000_0_54840   ribosomal RNA processing protein 41B, putative
Trypanosoma cruzi TcCLB.503653.30   RNase PH-like protein, putative
Trypanosoma cruzi TcCLB.505037.20   ribosomal RNA processing protein 41B, putative
Toxoplasma gondii TGME49_306610   3' exoribonuclease family, domain 1 domain-containing protein
Trichomonas vaginalis TVAG_287740   Exosome complex exonuclease RRP46, putative

Essentiality

TcCLB.503653.30 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.2.2180 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.2.2180 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.2.2180 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.2.2180 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C14A4.5 Caenorhabditis elegans larval arrest wormbase
CELE_C14A4.5 Caenorhabditis elegans slow growth wormbase
YGR095C Saccharomyces cerevisiae inviable yeastgenome
TGME49_306610 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.
  • 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.
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.

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User comments

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Gene identifier TcCLB.503653.30 (Trypanosoma cruzi), RNase PH-like protein, putative
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