Detailed view for LmjF.06.0460

Basic information

TDR Targets ID: 29434
Leishmania major, ATP-NAD kinase-like protein
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.6605 | Length (AA): 1276 | MW (Da): 135933 | 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

PF01513   ATP-NAD kinase

Gene Ontology

Mouse over links to read term descriptions.
GO:0019674   NAD metabolic process  
GO:0006741   NADP biosynthetic process  
GO:0003951   NAD+ kinase activity  
GO:0008152   metabolic process  

Metabolic Pathways

Nicotinate and nicotinamide metabolism (KEGG)
Global map (KEGG)

Structural information

Modbase 3D models:

There are 8 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
1014 1271 2an1 (A) 21 289 19.00 0 1 0.38 -0.11
1051 1273 1u0t (A) 76 298 22.00 0 1 0.32 -0.42
627 838 4w4i (A) 5 265 17.00 0 0.87 0.0461442 0.74
933 967 3bog (C) 3 73 49.00 0.04 0.09 0.383129 1.25
1027 1274 2i2c (A) 11 263 20.00 0.00000000083 1 0.393157 0.15
1039 1267 1z0s (A) 28 245 22.00 0.00000011 0.98 0.390267 0.21
1048 1195 2an1 (D) 61 206 32.00 0.00005 0.11 0.223687 1.35
1052 1249 1yt5 (A) 43 230 32.00 0.000000008 0.9 0.381872 0.45

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
Lower 20-40% percentile amastigotes. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile metacyclic. Fernandes MC
Show/Hide expression data references
  • Fernandes MC Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures.

Orthologs

Ortholog group members (OG5_136758)

Species Accession Gene Product
Entamoeba histolytica EHI_151920   inorganic polyphosphate/ATP-NAD kinase, putative
Leishmania braziliensis LbrM.06.0470   ATP-NAD kinase-like protein
Leishmania donovani LdBPK_060480.1   ATP-NAD kinase-like protein
Leishmania infantum LinJ.06.0480   ATP-NAD kinase-like protein
Leishmania major LmjF.06.0460   ATP-NAD kinase-like protein
Leishmania mexicana LmxM.06.0460   ATP-NAD kinase-like protein
Trypanosoma brucei gambiense Tbg972.7.5850   ATP-NAD kinase-like protein, putative
Trypanosoma brucei Tb927.7.5080   ATP-NAD kinase-like protein
Trypanosoma cruzi TcCLB.509151.40   inorganic polyphosphate/ATP-NAD kinase, putative
Trypanosoma cruzi TcCLB.508175.260   poly(p)/ATP NAD kinase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0400   inorganic polyphosphate/ATP-NAD kinase

Essentiality

LmjF.06.0460 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.7.5080 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.7.5080 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.7.5080 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.7.5080 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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.
  • 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.
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.

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

  • Assay for NAD+ Kinase (2.7.1.23 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

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 LmjF.06.0460 (Leishmania major), ATP-NAD kinase-like protein
Title for this comment
Comment