Detailed view for Tb927.4.460

Basic information

TDR Targets ID: 18848
Trypanosoma brucei, Alkylated DNA repair protein (alkB homolog), putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.6489 | Length (AA): 323 | MW (Da): 37656 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0

Druggability Group : DG3

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

PF13532   2OG-Fe(II) oxygenase superfamily

Gene Ontology

Mouse over links to read term descriptions.
GO:0016491   oxidoreductase activity  
GO:0055114   oxidation reduction  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
92 315 2iuw (A) 83 279 22.00 0 1 0.721598 0.13
97 313 4jht (A) 17 212 24.00 0 1 0.862927 -0.3
132 230 3u0p (E) 35 143 32.00 0.94 0.12 0.294602 1.58

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 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_129589)

Species Accession Gene Product
Arabidopsis thaliana AT1G11780   oxidoreductase, 2OG-Fe(II) oxygenase family protein
Babesia bovis BBOV_I002590   conserved hypothetical protein
Brugia malayi Bm1_35285   ALKBH protein
Caenorhabditis elegans CELE_Y51H7C.5   Protein Y51H7C.5
Dictyostelium discoideum DDB_G0285575   alkylated DNA repair protein
Drosophila melanogaster Dmel_CG33250   CG33250 gene product from transcript CG33250-RA
Echinococcus granulosus EgrG_000517300   alkylated DNA repair protein alkB
Echinococcus multilocularis EmuJ_000517300   conserved hypothetical protein
Homo sapiens ENSG00000100601   alkB, alkylation repair homolog 1 (E. coli)
Leishmania braziliensis LbrM.16.0360   hypothetical protein, conserved
Leishmania donovani LdBPK_160360.1   2OG-Fe(II) oxygenase superfamily, putative
Leishmania infantum LinJ.16.0360   hypothetical protein, conserved
Leishmania major LmjF.16.0350   hypothetical protein, conserved
Leishmania mexicana LmxM.16.0350   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_10203   ALKBH protein
Mus musculus 211064   alkB, alkylation repair homolog 1 (E. coli)
Oryza sativa 4350536   Os11g0488500
Schistosoma japonicum Sjp_0066530   ko:K10765 alkylated DNA repair protein alkB homolog 1, putative
Schistosoma mansoni Smp_041490   hypothetical protein
Schmidtea mediterranea mk4.004395.01  
Schmidtea mediterranea mk4.005057.00  
Trypanosoma brucei gambiense Tbg972.4.200   Alkylated DNA repair protein (alkB homolog), putative
Trypanosoma brucei Tb927.4.460   Alkylated DNA repair protein (alkB homolog), putative
Trypanosoma congolense TcIL3000_4_140   Alkylated DNA repair protein (alkB homolog), putative
Trypanosoma cruzi TcCLB.510687.140   alkylated DNA repair protein, putative
Theileria parva TP01_0030   hypothetical protein

Essentiality

Tb927.4.460 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.460 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.460 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.4.460 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.4.460 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) normal (PATO:0000461) 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: normal cell proliferation (no significant loss or 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 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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Gene identifier Tb927.4.460 (Trypanosoma brucei), Alkylated DNA repair protein (alkB homolog), putative
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