Detailed view for LmjF.28.2220

Basic information

TDR Targets ID: 29868
Leishmania major, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase-like
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.8695 | Length (AA): 833 | MW (Da): 89380 | 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

PF01676   Metalloenzyme superfamily
PF06094   Gamma-glutamyl cyclotransferase, AIG2-like
PF10143   2,3-bisphosphoglycerate-independent phosphoglycerate mutase

Gene Ontology

Mouse over links to read term descriptions.
GO:0046537   2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity  
GO:0046872   metal ion binding  
GO:0003824   catalytic activity  
GO:0008152   metabolic process  

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
5 175 1vkb (A) 1 137 25.00 0 0.57 0.15 -0.29
5 156 1vkb (A) 1 124 27.00 0 0.96 0.29 -0.17
711 765 2gso (A) 201 262 25.00 0.000043 0.16 0.25 -0.42
7 115 3jud (A) 3 113 39.00 0.00011 1 0.479352 -0.09
7 105 1v30 (A) 9 88 26.00 0 0.53 0.161848 0.01
257 832 2zkt (A) 5 409 35.00 0 1 0.165877 1.62
260 823 2zkt (B) 8 400 39.00 0 1 0.459571 1.17
566 661 4wbt (A) 28 125 41.00 0.84 0.04 0.107746 2.11

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, 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_131753)

Species Accession Gene Product
Arabidopsis thaliana AT3G30841   Cofactor-independent phosphoglycerate mutase
Arabidopsis thaliana AT4G09520   Cofactor-independent phosphoglycerate mutase
Dictyostelium discoideum DDB_G0277763   hypothetical protein
Leishmania braziliensis LbrM.28.2420   2,3-bisphosphoglycerate-independent phosphoglycerate mutase-like
Leishmania donovani LdBPK_282380.1   2,3-bisphosphoglycerate-independent phosphoglycerate mutase-like
Leishmania infantum LinJ.28.2380   2,3-bisphosphoglycerate-independent phosphoglycerate mutase-like
Leishmania major LmjF.28.2220   2,3-bisphosphoglycerate-independent phosphoglycerate mutase-like
Leishmania mexicana LmxM.28.2220   2,3-bisphosphoglycerate-independent phosphoglycerate mutase-like
Trypanosoma brucei gambiense Tbg972.11.12900   2,3-bisphosphoglycerate-independent phosphoglycerate mutase-like protein, putative
Trypanosoma brucei Tb927.11.11490   2,3-bisphosphoglycerate-independent phosphoglycerate mutase-like protein, putative
Trypanosoma congolense TcIL3000.11.12090   2,3-bisphosphoglycerate-independent phosphoglycerate mutase-like protein, putative
Trypanosoma cruzi TcCLB.511017.20   2,3-bisphosphoglycerate-independent phosphoglycerate mutase, putative
Trichomonas vaginalis TVAG_414300   2,3-bisphosphoglycerate-independent phosphoglycerate mutase, putative

Essentiality

LmjF.28.2220 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.3340 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.3340 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.3340 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.3340 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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
  • 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.

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 Phosphoglycerate Mutase (5.4.2.1 ) 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 mexicana ( 1 )

Reagent availability

  • Reagent:
  • Target Type Source Notes
    LmjF.28.2220 purified protein BRENDA A protein with this EC number or name or sequence has been purified from Leishmania mexicana ( 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.28.2220 (Leishmania major), 2,3-bisphosphoglycerate-independent phosphoglycerate mutase-like
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