Detailed view for LmjF.25.2370

Basic information

TDR Targets ID: 26139
Leishmania major, adenylate kinase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.915 | Length (AA): 234 | MW (Da): 25631 | 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

PF00406   Adenylate kinase
PF05191   Adenylate kinase, active site lid

Gene Ontology

Mouse over links to read term descriptions.
GO:0019205   nucleobase, nucleoside, nucleotide kinase activity  
GO:0016776   phosphotransferase activity, phosphate group as acceptor  
GO:0006139   nucleobase, nucleoside, nucleotide and nucleic acid metabolic process  
GO:0005524   ATP binding  
GO:0004017   adenylate kinase activity  

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
2 232 2ak3 (A) 2 212 36.00 0 1 1.36 -0.66
6 233 2eu8 (A) 1 215 34.00 0 1 1.4 -0.81
11 98 1qf9 (A) 12 94 34.00 0.00000011 1 0.83 -0.88
2 233 3adk (A) 5 193 28.00 0 1 1.09855 0.26
6 233 1zin (A) 1 215 37.00 0 1 1.39726 -0.38
6 233 3dl0 (A) 1 215 34.00 0 1 1.36546 -0.58
6 233 4mkg (A) 1 215 27.00 0 1 1.33146 -0.64
7 210 3tlx (D) 30 220 39.00 0.00000038 1 0.719695 0.87

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 amastigotes, 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_134283)

Species Accession Gene Product
Arabidopsis thaliana AT2G37250   adenosine kinase
Arabidopsis thaliana AT2G39270   probable adenylate kinase
Babesia bovis BBOV_IV008100   nucleoside monophosphate kinase
Leishmania braziliensis LbrM.25.1960   adenylate kinase, putative
Leishmania donovani LdBPK_252480.1   adenylate kinase, putative
Leishmania infantum LinJ.25.2480   adenylate kinase, putative
Leishmania major LmjF.25.2370   adenylate kinase, putative
Leishmania mexicana LmxM.25.2370   adenylate kinase, putative
Neospora caninum NCLIV_040820   Adenylate kinase (EC 2.7.4.3), related
Oryza sativa 4331502   Os03g0130400
Oryza sativa 4337358   Os04g0671100
Plasmodium berghei PBANKA_0717600   GTP:AMP phosphotransferase, putative
Plasmodium falciparum PF3D7_0415600   GTP:AMP phosphotransferase
Plasmodium knowlesi PKNH_0507200   GTP:AMP phosphotransferase, putative
Plasmodium vivax PVX_089735   adenylate kinase 1, putative
Plasmodium yoelii PY02813   adenylate kinase 1
Toxoplasma gondii TGME49_288320   adenylate kinase

Essentiality

LmjF.25.2370 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_0717600 Plasmodium berghei Slow plasmo
TGME49_288320 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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

Druggability index (range: 0 to 1): 0.3

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Plasmodium falciparum GTP:AMP phosphotransferase Compounds References
By sequence similarity to non orthologous druggable targets
Species Target Length Identity Alignment span Linked Drugs Reference
Rattus norvegicus Adenylate kinase 3 alpha like 1 227 aa 37.1% 210 aa Compounds References
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0133 0.456 1
0.0136 0.6105 1
0.0024 0.5361 0.5361

Assayability

Assay information

  • Assay for Myokinase (2.7.4.3 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.
  • BRENDA Assay
  • An enzyme with this EC number or name or sequence has been assayed in Leishmania donovani ( 1 )

Reagent availability

  • Reagent:
  • Target Type Source Notes
    LmjF.25.2370 purified protein BRENDA A protein with this EC number or name or sequence has been purified from Leishmania donovani ( 1 )

Bibliographic References

2 literature references were collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier LmjF.25.2370 (Leishmania major), adenylate kinase, putative
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