Detailed view for LmjF.27.0420

Basic information

TDR Targets ID: 28308
Leishmania major, ribokinase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.8662 | Length (AA): 329 | MW (Da): 35342 | 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

PF00294   pfkB family carbohydrate kinase

Gene Ontology

Mouse over links to read term descriptions.
GO:0016301   kinase activity  
GO:0004747   ribokinase activity  
GO:0006014   D-ribose metabolic process  

Metabolic Pathways

Pentose phosphate pathway (KEGG)

Structural information

Modbase 3D models:

There are 6 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
15 329 1vm7 (A) 2 297 34.00 0 1 1.31 -0.96
18 325 2fv7 (A) 18 318 41.00 0 1 1.55 -1.52
15 326 1rkd (A) 4 303 38.00 0 1 1.46313 -0.84
15 328 4xda (A) 1 302 36.00 0 1 1.45831 -1
15 328 3go6 (A) 13 296 33.00 0 1 1.25421 -0.19
18 325 5bye (B) 18 318 41.00 0 1 1.43597 -0.89

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 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_127229)

Species Accession Gene Product
Arabidopsis thaliana AT1G17160   pfkB-like carbohydrate kinase family protein
Brugia malayi Bm1_23645   Ribokinase
Candida albicans CaO19.6344   similar to Ribokinase
Candida albicans CaO19.13700   similar to Ribokinase
Caenorhabditis elegans CELE_F07A11.5   Protein F07A11.5
Dictyostelium discoideum DDB_G0280893   ATP:D-ribose 5-phosphotransferase
Drosophila melanogaster Dmel_CG17010   CG17010 gene product from transcript CG17010-RA
Drosophila melanogaster Dmel_CG13369   CG13369 gene product from transcript CG13369-RA
Escherichia coli b3752   ribokinase
Echinococcus granulosus EgrG_000853000   ribokinase
Entamoeba histolytica EHI_138020   ribokinase, putative
Echinococcus multilocularis EmuJ_000853000   ribokinase
Giardia lamblia GL50803_15297   Ribokinase
Homo sapiens 64080   ribokinase
Leishmania braziliensis LbrM.27.0510   ribokinase, putative
Leishmania donovani LdBPK_270430.1   ribokinase, putative
Leishmania infantum LinJ.27.0430   ribokinase, putative
Leishmania major LmjF.27.0420   ribokinase, putative
Leishmania mexicana LmxM.27.0420   ribokinase, putative
Loa Loa (eye worm) LOAG_04812   hypothetical protein
Mus musculus ENSMUSG00000029136   ribokinase
Mycobacterium tuberculosis Rv2436   Ribokinase RbsK
Neospora caninum NCLIV_001280   ribokinase, putative
Oryza sativa 4326855   Os01g0665400
Onchocerca volvulus OVOC11423   Ribokinase homolog
Saccharomyces cerevisiae YCR036W   Rbk1p
Schistosoma japonicum Sjp_0048490   ko:K00852 ribokinase [EC2.7.1.15], putative
Schistosoma mansoni Smp_044850   ribokinase
Schmidtea mediterranea mk4.001782.01   Putative ribokinase
Schmidtea mediterranea mk4.011260.00   Putative ribokinase
Schmidtea mediterranea mk4.002563.00   Putative ribokinase
Trypanosoma brucei gambiense Tbg972.11.1090   ribokinase, putative
Trypanosoma brucei Tb11.v5.0729   ribokinase, putative
Trypanosoma brucei Tb927.11.1020   ribokinase, putative
Trypanosoma congolense TcIL3000.11.930   ribokinase, putative
Trypanosoma cruzi TcCLB.506925.480   ribokinase, putative
Toxoplasma gondii TGME49_305030   kinase, pfkB family protein
Trichomonas vaginalis TVAG_384480   ribokinase, putative
Trichomonas vaginalis TVAG_365110   ribokinase, putative

Essentiality

LmjF.27.0420 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.03.0090 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.03.0090 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.03.0090 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.03.0090 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b3752 Escherichia coli non-essential goodall
TGME49_305030 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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.

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): 0.2

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
Species Target Length Identity Alignment span Linked Drugs Reference
Burkholderia cepacia (strain J2315 / LMG 16656) (Burkholderiacenocepacia (strain J2315)) D-beta-D-heptose 7-phosphate kinase 316 aa 23.5% 302 aa Compounds References
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

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

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Gene identifier LmjF.27.0420 (Leishmania major), ribokinase, putative
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