Detailed view for TcCLB.503579.30

Basic information

TDR Targets ID: 41493
Trypanosoma cruzi, DNA polymerase sigma-like protein, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 9.4158 | Length (AA): 465 | MW (Da): 52037 | 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

No Pfam domain information for this protein.

Gene Ontology

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

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 6 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
71 465 1q79 (A) 20 407 12.00 0 0.79 0.68 0.01
242 425 2b4v (A) 264 471 17.00 0.0000000000031 0.29 0.37 -0.94
15 348 3pq1 (B) 63 491 18.00 0 1 0.69438 0.48
81 398 3nyb (A) 165 456 23.00 0 1 0.709971 0.38
91 341 3nyb (A) 179 389 28.00 0.0000000023 1 0.610485 0.51
214 369 5w0o (A) 1087 1283 34.00 0.0000038 0.78 0.399184 0.96

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 metacyclic. Smircich P
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile epimastigote. 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_147051)

Species Accession Gene Product
Leishmania braziliensis LbrM.26.0510   DNA polymerase sigma-like protein
Leishmania donovani LdBPK_260480.1   DNA polymerase sigma-like protein
Leishmania infantum LinJ.26.0480   DNA polymerase sigma-like protein
Leishmania mexicana LmxM.26.0490   DNA polymerase sigma-like protein
Trypanosoma brucei gambiense Tbg972.7.1440   DNA polymerase sigma-like protein
Trypanosoma brucei Tb927.7.1440   non-canonical poly (A) polymerase
Trypanosoma congolense TcIL3000_0_29370   non-canonical poly (A) polymerase
Trypanosoma cruzi TcCLB.503579.30   DNA polymerase sigma-like protein, putative
Trypanosoma cruzi TcCLB.507517.20   DNA polymerase sigma-like protein, putative

Essentiality

TcCLB.503579.30 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.7.1440 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.7.1440 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.7.1440 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.7.1440 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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.
  • 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

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 TcCLB.503579.30 (Trypanosoma cruzi), DNA polymerase sigma-like protein, putative
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