Detailed view for Tb927.9.3970

Basic information

TDR Targets ID: 10629
Trypanosoma brucei, nicotinamidase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.731 | Length (AA): 204 | MW (Da): 22391 | Paralog Number: 1

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

PF00857   Isochorismatase family

Gene Ontology

Mouse over links to read term descriptions.
GO:0005575   cellular_component  
GO:0003824   catalytic activity  
GO:0016787   hydrolase activity  
GO:0008152   metabolic process  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
6 203 3r2j (A) 19 213 45.00 0 1 1.65029 -1.48

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
Mid 40-60% percentile Procyclic. Siegel TN
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile 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_127752)

Species Accession Gene Product
Candida albicans CaO19.14000   pyrazinamidase/nicotinamidase
Candida albicans CaO19_6684   hypothetical protein
Candida albicans CaO19.6684   pyrazinamidase/nicotinamidase
Candida albicans CaO19.6708   pyrazinamidase/nicotinamidase
Candida albicans CaO19.13976   pyrazinamidase/nicotinamidase
Caenorhabditis elegans CELE_Y38C1AA.3   Protein PNC-1, isoform B
Caenorhabditis elegans CELE_Y57G11C.47   Protein PNC-2
Dictyostelium discoideum DDB_G0293618   hypothetical protein
Dictyostelium discoideum DDB_G0271336   hypothetical protein
Drosophila melanogaster Dmel_CG31216   Nicotinamide amidase
Escherichia coli b1768   nicotinamidase/pyrazinamidase
Giardia lamblia GL50803_6757   Pyrazinamidase/nicotinamidase
Leishmania braziliensis LbrM.01.0500   alpha/beta-hydrolase-like protein
Leishmania donovani LdBPK_010470.1   alpha/beta-hydrolase-like protein
Leishmania infantum LinJ.01.0470   alpha/beta-hydrolase-like protein
Leishmania major LmjF.01.0450   alpha/beta-hydrolase-like protein
Leishmania mexicana LmxM.01.0450   alpha/beta-hydrolase-like protein
Mycobacterium tuberculosis Rv2043c   Pyrazinamidase/nicotinamidase PncA (PZase)
Mycobacterium ulcerans MUL_2257   pyrazinamidase/nicotinamidase, PncA
Neospora caninum NCLIV_023670   pyrazinamidase/nicotinamidase, putative
Plasmodium berghei PBANKA_1218000   nicotinamidase, putative
Plasmodium falciparum PF3D7_0320500   nicotinamidase, putative
Plasmodium knowlesi PKNH_0820300   nicotinamidase, putative
Plasmodium vivax PVX_095210   nicotinamidase, putative
Plasmodium yoelii PY05269   isochorismatase family protein, putative
Saccharomyces cerevisiae YGL037C   nicotinamidase
Schmidtea mediterranea mk4.062833.00  
Trypanosoma brucei gambiense Tbg972.9.2100   pyrazinamidase/nicotinamidase, putative
Trypanosoma brucei Tb927.9.4040   nicotinamidase, putative
Trypanosoma brucei Tb927.9.3970   nicotinamidase, putative
Trypanosoma congolense TcIL3000_0_18470   nicotinamidase, putative
Trypanosoma cruzi TcCLB.506593.60   nicotinamidase, putative
Trypanosoma cruzi TcCLB.506829.80   nicotinamidase, putative
Toxoplasma gondii TGME49_281990   Nicotinamidase
Trichomonas vaginalis TVAG_366320   pyrazinamidase/nicotinamidase, putative

Essentiality

Tb927.9.3970 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2075 Mycobacterium tuberculosis non-essential nmpdr
Tb09.160.2540 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.160.2540 this record Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb09.160.2540 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.160.2540 this record Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
b1768 Escherichia coli non-essential goodall
PBANKA_1218000 Plasmodium berghei Dispensable plasmo
TGME49_281990 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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
  • 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

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 3 days). References: 21363968
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 Tb927.9.3970 (Trypanosoma brucei), nicotinamidase, putative
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