Detailed view for LmjF.11.0210

Basic information

TDR Targets ID: 26507
Leishmania major, acidocalcisomal pyrophosphatase
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.2634 | Length (AA): 443 | MW (Da): 50994 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | 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

PF00719   Inorganic pyrophosphatase

Gene Ontology

Mouse over links to read term descriptions.
GO:0005737   cytoplasm  
GO:0005509   calcium ion binding  
GO:0004427   inorganic diphosphatase activity  
GO:0000287   magnesium ion binding  
GO:0006796   phosphate metabolic process  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
103 172 2ami (A) 6 76 26.00 0.000000000027 0.99 0.67 -2.08
207 434 1e9g (A) 12 229 48.00 0 1 1.08 -0.82
209 442 1e9g (A) 1 237 39.00 0 1 1.02 -0.76
9 169 3u0k (A) 277 440 18.00 0.0000000067 0.48 0.555331 -0.06
42 437 5cuy (A) 20 408 66.00 0 1 1.65591 -0.18
57 443 5cuv (A) 34 414 69.00 0 1 1.67559 -0.28
109 169 2m97 (A) 5 66 23.00 0 0.96 0.573398 -1.48
116 169 2ami (A) 19 73 30.00 0.9 0.68 0.535796 -0.68

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 metacyclic. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile amastigotes. 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_127487)

Species Accession Gene Product
Arabidopsis thaliana AT5G09650   soluble inorganic pyrophosphatase 1
Babesia bovis BBOV_III010840   inorganic pyrophosphatase family protein
Brugia malayi Bm1_16955   inorganic pyrophosphatase
Candida albicans CaO19.3590   inorganic pyrophosphatase
Candida albicans CaO19.11072   inorganic pyrophosphatase
Caenorhabditis elegans CELE_C47E12.4   Protein PYP-1, isoform D
Cryptosporidium hominis Chro.40159   inorganic pyrophosphatase precursor
Cryptosporidium parvum cgd4_1400   conserved hypothetical protein
Dictyostelium discoideum DDB_G0284265   inorganic pyrophosphatase
Drosophila melanogaster Dmel_CG4634   Nucleosome remodeling factor - 38kD
Entamoeba histolytica EHI_124880   inorganic pyrophosphatase, putative
Homo sapiens ENSG00000138777   pyrophosphatase (inorganic) 2
Homo sapiens ENSG00000180817   pyrophosphatase (inorganic) 1
Leishmania braziliensis LbrM.19.0110   acidocalcisomal pyrophosphatase
Leishmania donovani LdBPK_110210.1   acidocalcisomal pyrophosphatase
Leishmania infantum LinJ.11.0210   acidocalcisomal pyrophosphatase
Leishmania major LmjF.11.0210   acidocalcisomal pyrophosphatase
Leishmania mexicana LmxM.11.0210   acidocalcisomal pyrophosphatase
Loa Loa (eye worm) LOAG_03390   inorganic pyrophosphatase
Mus musculus ENSMUSG00000028013   pyrophosphatase (inorganic) 2
Mus musculus ENSMUSG00000020089   pyrophosphatase (inorganic) 1
Neospora caninum NCLIV_028850   soluble inorganic pyrophosphatase, putative
Oryza sativa 4330852   Os02g0768600
Plasmodium berghei PBANKA_0414100   inorganic pyrophosphatase, putative
Plasmodium falciparum PF3D7_0316300   inorganic pyrophosphatase, putative
Plasmodium knowlesi PKNH_0825800   inorganic pyrophosphatase, putative
Plasmodium vivax PVX_095420   inorganic pyrophosphatase, putative
Plasmodium yoelii PY03581   inorganic pyrophosphatase, putative
Saccharomyces cerevisiae YBR011C   inorganic diphosphatase IPP1
Schmidtea mediterranea mk4.000077.06  
Trypanosoma brucei gambiense Tbg972.11.8000   acidocalcisomal pyrophosphatase, putative
Trypanosoma brucei gambiense Tbg972.11.8020   acidocalcisomal pyrophosphatase, putative
Trypanosoma brucei Tb927.11.7060   acidocalcisomal pyrophosphatase
Trypanosoma brucei Tb927.11.7080   acidocalcisomal pyrophosphatase
Trypanosoma congolense TcIL3000_0_38820   acidocalcisomal pyrophosphatase
Trypanosoma congolense TcIL3000.11.7660   acidocalcisomal pyrophosphatase
Trypanosoma cruzi TcCLB.511165.40   acidocalcisomal pyrophosphatase, putative
Trypanosoma cruzi TcCLB.503613.60   acidocalcisomal pyrophosphatase, putative
Toxoplasma gondii TGME49_283830   type I inorganic pyrophosphatase PPase
Theileria parva TP02_0061   inorganic pyrophosphatase, putative

Essentiality

LmjF.11.0210 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.02.4930 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.02.4930 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.02.4930 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.02.4930 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Tb11.02.4910 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.02.4910 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.02.4910 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.02.4910 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C47E12.4 Caenorhabditis elegans embryonic lethal wormbase
CELE_C47E12.4 Caenorhabditis elegans larval arrest wormbase
CELE_C47E12.4 Caenorhabditis elegans larval lethal wormbase
CELE_C47E12.4 Caenorhabditis elegans slow growth wormbase
CELE_C47E12.4 Caenorhabditis elegans sterile wormbase
YBR011C Saccharomyces cerevisiae inviable yeastgenome
TGME49_283830 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell differentiation (GO:0030154) disrupted (PATO:0001507) single cell organism (CARO:0000064) promastigote (BTO:0001124) inferred from bioassay (ECO:0000094) Leishmania amazonensis No drug identifiers listed for this gene.
Annotator: crowther@u.washington.edu. Comment: Dominant negative genetic disruption of LaVSP1 reduces metacyclogenesis and virulence in mice; . References: 16291745
viability (PATO:0000169) decreased (PATO:0000468) single cell organism (CARO:0000064) amastigote (BTO:0000062) host (GO:0018995) Leishmania amazonensis No drug identifiers listed for this gene.
Annotator: crowther@u.washington.edu. Comment: Dominant negative genetic disruption of LaVSP1 reduces metacyclogenesis and virulence in mice; . References: 16291745
viability (PATO:0000169) decreased (PATO:0000468) single cell organism (CARO:0000064) amastigote (BTO:0000062) inferred from bioassay (ECO:0000094) Leishmania amazonensis No drug identifiers listed for this gene.
Annotator: crowther@u.washington.edu. Comment: Dominant negative genetic disruption of LaVSP1 reduces metacyclogenesis and virulence in mice; . References: 16291745

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
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

  • Lmaj006923AAA;
  • Type Source Notes
    soluble recombinant protein Structural Genomics for Pathogenic Protozoa (SGPP) Lmaj006923; Recombinant protein: full-length; Source: L major; acidocalcisomal pyrophosphatase ;

Bibliographic References

No literature references available for this target.

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Gene identifier LmjF.11.0210 (Leishmania major), acidocalcisomal pyrophosphatase
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