Detailed view for LmjF.36.1960

Basic information

TDR Targets ID: 26611
Leishmania major, phosphomannomutase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 4.9652 | Length (AA): 247 | MW (Da): 28101 | 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

PF03332   Eukaryotic phosphomannomutase

Gene Ontology

Mouse over links to read term descriptions.
GO:0009298   GDP-mannose biosynthetic process  
GO:0005737   cytoplasm  
GO:0004615   phosphomannomutase activity  
GO:0003824   catalytic activity  
GO:0019307   mannose biosynthetic process  
GO:0008152   metabolic process  

Structural information

Modbase 3D models:

There are 3 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
2 244 2amy (A) 4 246 52.00 0 1 1.69 -1.78
4 242 2fue (A) 13 253 51.00 0 1 1.74 -1.83
4 245 2i54 (A) 4 245 94.00 0 1 2.22436 -2.12

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:

PDB tag
  • 2I54:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 2I55:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile amastigotes. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Upper 60-80% 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_127648)

Species Accession Gene Product
Arabidopsis thaliana AT2G45790   phosphomannomutase
Babesia bovis BBOV_IV009850   phosphomannomutase, putative
Brugia malayi Bm1_38705   phosphomannomutase 2
Candida albicans CaO19.2937   phosphomannomutase that can functionally substitute for S. cerevisiae SEC53 (YFL045C)
Candida albicans CaO19.10454   phosphomannomutase that can functionally substitute for S. cerevisiae SEC53 (YFL045C)
Caenorhabditis elegans CELE_F52B11.2   Protein F52B11.2, isoform B
Cryptosporidium hominis Chro.40115   hypothetical protein
Cryptosporidium parvum cgd4_960   phosphomannomutase
Dictyostelium discoideum DDB_G0272781   phosphomannomutase B
Dictyostelium discoideum DDB_G0279289   hypothetical protein
Drosophila melanogaster Dmel_CG10688   CG10688 gene product from transcript CG10688-RA
Echinococcus granulosus EgrG_000927400   phosphomannomutase
Entamoeba histolytica EHI_179810   phosphomannomutase, putative
Echinococcus multilocularis EmuJ_000927400   phosphomannomutase
Homo sapiens ENSG00000140650   phosphomannomutase 2
Homo sapiens ENSG00000100417   phosphomannomutase 1
Leishmania braziliensis LbrM.35.2180   phosphomannomutase, putative
Leishmania donovani LdBPK_362070.1   phosphomannomutase, putative
Leishmania infantum LinJ.36.2070   phosphomannomutase, putative
Leishmania major LmjF.36.1960   phosphomannomutase, putative
Leishmania mexicana LmxM.36.1960   phosphomannomutase, putative
Loa Loa (eye worm) LOAG_11718   phosphomannomutase 2
Mus musculus ENSMUSG00000022711   phosphomannomutase 2
Mus musculus ENSMUSG00000022474   phosphomannomutase 1
Neospora caninum NCLIV_016330   phosphomannomutase 2, putative
Oryza sativa 4337437   Os04g0682300
Onchocerca volvulus OVOC4799   Putative phosphomannomutase
Plasmodium berghei PBANKA_0501700   phosphomannomutase, putative
Plasmodium falciparum PF3D7_1017400   phosphomannomutase, putative
Plasmodium knowlesi PKNH_0601600   phosphomannomutase, putative
Plasmodium vivax PVX_001740   phosphomannomutase, putative
Plasmodium yoelii PY00199   Eukaryotic phosphomannomutase
Saccharomyces cerevisiae YFL045C   phosphomannomutase SEC53
Schistosoma japonicum Sjp_0081430   ko:K01840 phosphomannomutase [EC5.4.2.8], putative
Schistosoma japonicum Sjp_0081440   IPR005002,Eukaryotic phosphomannomutase,domain-containing
Schistosoma mansoni Smp_087860   phosphomannomutase
Schmidtea mediterranea mk4.001409.00   Probable phosphomannomutase
Schmidtea mediterranea mk4.000173.04   Phosphomannomutase
Trypanosoma brucei gambiense Tbg972.10.7890   phosphomannomutase, putative
Trypanosoma brucei Tb927.10.6440   phosphomannomutase
Trypanosoma congolense TcIL3000_10_5500   phosphomannomutase, putative
Trypanosoma cruzi TcCLB.510187.480   phosphomannomutase, putative
Toxoplasma gondii TGME49_239710   phosphomannomutase
Theileria parva TP01_0785   phosphomannomutase, putative
Trichomonas vaginalis TVAG_111700   phosphomannomutase, putative

Essentiality

LmjF.36.1960 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.6440 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.6440 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.6440 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.6440 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F52B11.2 Caenorhabditis elegans slow growth wormbase
YFL045C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0501700 Plasmodium berghei Dispensable plasmo
TGME49_239710 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
viability (PATO:0000169) absent (PATO:0000462) single cell organism (CARO:0000064) amastigote (BTO:0000062) inferred from loss-of-function mutant phenotype (ECO:0000016) Leishmania mexicana No drug identifiers listed for this gene.
Annotator: aaronjr@u.washington.edu. Comment: L. mexicana DeltaPMM are largely devoid of all known Man-containing glycoconjugates and are unable to establish an infection in mouse macrophages or the living animal. References: 11689705
viability (PATO:0000169) absent (PATO:0000462) single cell organism (CARO:0000064) amastigote (BTO:0000062) inferred from bioassay (ECO:0000094) Leishmania mexicana No drug identifiers listed for this gene.
Annotator: aaronjr@u.washington.edu. Comment: L. mexicana DeltaPMM are largely devoid of all known Man-containing glycoconjugates and are unable to establish an infection in mouse macrophages or the living animal. References: 11689705
viability (PATO:0000169) absent (PATO:0000462) single cell organism (CARO:0000064) amastigote (BTO:0000062) host (GO:0018995) Leishmania mexicana No drug identifiers listed for this gene.
Annotator: aaronjr@u.washington.edu. Comment: L. mexicana DeltaPMM are largely devoid of all known Man-containing glycoconjugates and are unable to establish an infection in mouse macrophages or the living animal. References: 11689705
viability (PATO:0000169) absent (PATO:0000462) single cell organism (CARO:0000064) amastigote (BTO:0000062) inferred from loss-of-function mutant phenotype (ECO:0000016) Leishmania major No drug identifiers listed for this gene.
Annotator: aaronjr@u.washington.edu. Comment: L. major PMM knockouts are avirulent. References: 16963079
viability (PATO:0000169) absent (PATO:0000462) single cell organism (CARO:0000064) amastigote (BTO:0000062) inferred from bioassay (ECO:0000094) Leishmania major No drug identifiers listed for this gene.
Annotator: aaronjr@u.washington.edu. Comment: L. major PMM knockouts are avirulent. References: 16963079
viability (PATO:0000169) absent (PATO:0000462) single cell organism (CARO:0000064) amastigote (BTO:0000062) host (GO:0018995) Leishmania major No drug identifiers listed for this gene.
Annotator: aaronjr@u.washington.edu. Comment: L. major PMM knockouts are avirulent. References: 16963079

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
Species Known druggable target Linked compounds Reference
Homo sapiens phosphomannomutase 2 Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0052 0.3802 0
0.0052 0.2516 0

Assayability

Assay information

  • Assay for D-Fructose-1,6-Diphosphatase (3.1.3.11 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

No reagent availability information for this target.

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.36.1960 (Leishmania major), phosphomannomutase, putative
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