Detailed view for Tb927.9.11260

Basic information

TDR Targets ID: 18193
Trypanosoma brucei, nucleoside diphosphate kinase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.5809 | Length (AA): 334 | MW (Da): 37107 | 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

PF00334   Nucleoside diphosphate kinase

Gene Ontology

Mouse over links to read term descriptions.
GO:0005524   ATP binding  
GO:0004550   nucleoside diphosphate kinase activity  
GO:0006241   CTP biosynthetic process  
GO:0006228   UTP biosynthetic process  
GO:0006183   GTP biosynthetic process  

Structural information

Modbase 3D models:

There are 4 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
190 332 1ehw (A) 0 138 29.00 0 1 0.795944 -0.36
191 332 1s57 (A) 80 217 27.00 0 1 0.80895 -0.42
195 332 3ztp (A) 4 140 37.00 0 1 0.962974 -0.88
195 329 4ane (A) 3 134 30.00 0 1 0.869992 -0.94

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 Bloodstream Form. Siegel TN
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Procyclic. 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_130669)

Species Accession Gene Product
Drosophila melanogaster Dmel_CG8362   CG8362 gene product from transcript CG8362-RA
Echinococcus granulosus EgrG_000443700   non metastatic cells 7 protein expressed
Echinococcus multilocularis EmuJ_000443700   non metastatic cells 7, protein expressed
Giardia lamblia GL50803_14135   Nucleoside diphosphate kinase
Homo sapiens ENSG00000143156   NME/NM23 family member 7
Leishmania braziliensis LbrM.34.3850   nucleoside diphosphate kinase, putative
Leishmania donovani LdBPK_353910.1   nucleoside diphosphate kinase, putative
Leishmania infantum LinJ.35.3910   nucleoside diphosphate kinase, putative
Leishmania major LmjF.35.3870   nucleoside diphosphate kinase, putative
Leishmania mexicana LmxM.34.3870   nucleoside diphosphate kinase, putative
Mus musculus ENSMUSG00000026575   NME/NM23 family member 7
Neospora caninum NCLIV_022680   nucleoside diphosphate kinase 7, putative
Schistosoma japonicum Sjp_0308330   ko:K00940 nucleoside-diphosphate kinase [EC2.7.4.6], putative
Schistosoma japonicum Sjp_0107470   ko:K00940 nucleoside-diphosphate kinase [EC2.7.4.6], putative
Schistosoma mansoni Smp_153530   nucleoside diphosphate kinase
Schmidtea mediterranea mk4.001663.02   Nucleoside diphosphate kinase 7
Schmidtea mediterranea mk4.010719.04   Nucleoside diphosphate kinase 7
Trypanosoma brucei gambiense Tbg972.9.6720   nucleoside diphosphate kinase, putative
Trypanosoma brucei Tb927.9.11260   nucleoside diphosphate kinase, putative
Trypanosoma congolense TcIL3000_9_4640   nucleoside diphosphate kinase, putative
Trypanosoma cruzi TcCLB.508461.400   nucleoside diphosphate kinase
Toxoplasma gondii TGME49_202210   nucleoside diphosphate kinase
Trichomonas vaginalis TVAG_487510   nucleoside diphosphate kinase, putative
Trichomonas vaginalis TVAG_498410   nucleoside diphosphate kinase, putative

Essentiality

Tb927.9.11260 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.2560 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.211.2560 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb09.211.2560 this record Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb09.211.2560 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
TGME49_202210 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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

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) 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 procyclic forms . 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

  • Assay for Nucleoside 5'-Diphosphate Kinase (2.7.4.6 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

  • Reagent:
  • Target Type Source Notes
    Tb927.9.11260 cloned gene BRENDA A gene with this EC number or name or sequence has been cloned from Trypanosoma brucei ( 1 )

Bibliographic References

3 literature references were collected for this gene.

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Gene identifier Tb927.9.11260 (Trypanosoma brucei), nucleoside diphosphate kinase, putative
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