Detailed view for Tb927.5.3900

Basic information

TDR Targets ID: 20746
Trypanosoma brucei, Galactose oxidase, central domain/Domain of unknown function (DUF4110), putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.0431 | Length (AA): 744 | MW (Da): 82987 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | 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

PF13415   Galactose oxidase, central domain
PF13418   Galactose oxidase, central domain
PF13422   Domain of unknown function (DUF4110)

Gene Ontology

Mouse over links to read term descriptions.
GO:0005515   protein binding  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
71 401 5a10 (A) 12 323 24.00 0.00000044 0.89 0.583792 0.66
100 352 5gqt (A) 181 390 30.00 0.0015 0.92 0.351954 1.46
176 406 2uvk (A) 40 268 27.00 0.062 1 0.348384 1.18
663 744 4fqg (A) 56 142 17.00 0 0.12 0.373115 -1.63
673 739 4ihj (E) 55 121 21.00 0 0.04 0.472954 -1.9

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 Procyclic, Bloodstream Form. Siegel TN
Show/Hide expression data references
  • Siegel TN Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites.

Orthologs

Ortholog group members (OG5_129091)

Species Accession Gene Product
Arabidopsis thaliana AT5G50310   kelch repeat-containing protein
Babesia bovis BBOV_III006990   kelch repeat containing protein
Candida albicans CaO19.12476   Kelch-repeat
Candida albicans CaO19.5009   Kelch-repeat
Cryptosporidium hominis Chro.70399   Kelch repeats protein family
Cryptosporidium parvum cgd7_3580   kelch repeats protein
Drosophila melanogaster Dmel_CG4069   CG4069 gene product from transcript CG4069-RA
Homo sapiens ENSG00000104731   kelch domain containing 4
Leishmania braziliensis LbrM.16.0090   hypothetical protein, conserved
Leishmania donovani LdBPK_160090.1   Galactose oxidase, central domain/Domain of unknown function (DUF4110), putative
Leishmania infantum LinJ.16.0090   hypothetical protein, conserved
Leishmania major LmjF.16.0080   hypothetical protein, conserved
Leishmania mexicana LmxM.16.0080   hypothetical protein, conserved
Mus musculus ENSMUSG00000040263   kelch domain containing 4
Neospora caninum NCLIV_030210   Tip elongation aberrant protein 1, related
Oryza sativa 4336203   Os04g0483600
Plasmodium berghei PBANKA_0506800   kelch domain-containing protein, putative
Plasmodium falciparum PF3D7_1022600   kelch domain-containing protein, putative
Plasmodium knowlesi PKNH_0606900   kelch domain-containing protein, putative
Plasmodium vivax PVX_111590   kelch domain-containing protein
Plasmodium yoelii PY01661   Arabidopsis thaliana MXI22.1-related
Saccharomyces cerevisiae YPL263C   Kel3p
Trypanosoma brucei gambiense Tbg972.5.5410   hypothetical protein, conserved
Trypanosoma brucei Tb927.5.3900   Galactose oxidase, central domain/Domain of unknown function (DUF4110), putative
Trypanosoma congolense TcIL3000_5_4430   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.504251.30   Galactose oxidase, central domain/Domain of unknown function (DUF4110), putative
Trypanosoma cruzi TcCLB.506947.20   Galactose oxidase, central domain/Domain of unknown function (DUF4110), putative
Toxoplasma gondii TGME49_229290   kelch repeat-containing protein
Theileria parva TP04_0608   hypothetical protein

Essentiality

Tb927.5.3900 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.5.3900 this record Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.5.3900 this record Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.5.3900 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.5.3900 this record Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
TGME49_229290 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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.
  • 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
  • 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.
  • 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
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) increased (PATO:0000470) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: increased cell proliferation (significant gain of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) normal (PATO:0000461) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in procyclic forms . References: 21363968
cell proliferation (GO:0008283) increased (PATO:0000470) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: increased cell proliferation (significant gain of fitness) in differentiation of procyclic to bloodstream forms . References: 21363968

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

1 literature reference was collected for this gene.

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User comments

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Gene identifier Tb927.5.3900 (Trypanosoma brucei), Galactose oxidase, central domain/Domain of unknown function (DUF4110), putative
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