Detailed view for TcCLB.511003.140

Basic information

TDR Targets ID: 35131
Trypanosoma cruzi, vacuolar transport protein 4A, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.3453 | Length (AA): 448 | MW (Da): 49708 | 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

PF00004   ATPase family associated with various cellular activities (AAA)
PF09336   Vps4 C terminal oligomerisation domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0017111   nucleoside-triphosphatase activity  
GO:0005524   ATP binding  
GO:0000166   nucleotide binding  

Metabolic Pathways

Endocytosis (KEGG)

Structural information

Modbase 3D models:

There are 10 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
1 423 1e32 (A) 59 458 24.00 0 1 0.98 0.4
134 358 2ce7 (A) 151 379 36.00 0 1 0.97 -0.84
137 438 1xwi (A) 127 435 42.00 0 1 1.2 -0.53
30 389 3cf2 (A) 85 451 25.00 0 1 0.993671 0.92
124 442 4l15 (A) 296 583 32.00 0 1 0.971154 0.11
138 442 1xwi (A) 128 439 38.00 0 1 1.1169 0.01
141 371 5eqt (A) 103 341 36.00 0 1 0.929325 -0.3
141 440 2qp9 (X) 130 429 42.00 0 1 1.09474 0
145 363 5wc1 (A) 194 415 42.00 0 1 0.838539 0.44
308 363 4a3v (B) 379 433 15.00 0 0.25 0.3141 -0.52

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_147505)

Species Accession Gene Product
Leishmania braziliensis LbrM.20.2940   ATPase-like protein
Leishmania donovani LdBPK_343130.1   ATPase-like protein
Leishmania infantum LinJ.34.3130   ATPase-like protein
Leishmania major LmjF.34.3350   ATPase-like protein
Leishmania mexicana LmxM.33.3350   ATPase-like protein
Trypanosoma brucei gambiense Tbg972.4.1230   vacuolar transport protein 4A, putative
Trypanosoma brucei Tb927.4.1400   vacuolar transport protein 4A, putative
Trypanosoma cruzi TcCLB.511003.140   vacuolar transport protein 4A, putative

Essentiality

TcCLB.511003.140 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.1400 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.1400 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.4.1400 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.4.1400 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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
  • 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
  • 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
  • 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
  • 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

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

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier TcCLB.511003.140 (Trypanosoma cruzi), vacuolar transport protein 4A, putative
Title for this comment
Comment