Detailed view for LmjF.23.1480

Basic information

TDR Targets ID: 26853
Leishmania major, alanine racemase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.199 | Length (AA): 245 | MW (Da): 27135 | 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

PF01168   Alanine racemase, N-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0030170   pyridoxal phosphate binding  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 5 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
3 242 1bd0 (A) 5 231 16.00 0 1 1.17 -0.38
6 237 1ct5 (A) 6 246 42.00 0 1 1.49 -1.46
6 239 3r79 (A) 2 220 35.00 0 1 1.4221 -0.84
13 237 1ct5 (A) 13 246 44.00 0 1 1.55637 -1.76
26 239 3r79 (A) 18 220 45.00 0 1 1.37667 -0.6

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 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_127174)

Species Accession Gene Product
Arabidopsis thaliana AT4G26860   putative pyridoxal phosphate-dependent enzyme, YBL036C type
Arabidopsis thaliana AT1G11930   putative pyridoxal phosphate-dependent enzyme, YBL036C type
Brugia malayi Bm1_39750   Hypothetical UPF0001 protein F09E5.8 in chromosome II, putative
Candida albicans CaO19.2794   similar to family of uncharacterized enzymes that bind to pyridoxal-5'-phosphate.
Candida albicans CaO19.10312   similar to family of uncharacterized enzymes that bind to pyridoxal-5'-phosphate.
Caenorhabditis elegans CELE_F09E5.7   Protein F09E5.7
Caenorhabditis elegans CELE_F09E5.8   Protein F09E5.8
Cryptosporidium hominis Chro.50329   hypothetical protein
Cryptosporidium parvum cgd5_620   conserved hypothetical protein
Dictyostelium discoideum DDB_G0278713   alanine racemase N-terminal domain-containing protein
Drosophila melanogaster Dmel_CG1983   CG1983 gene product from transcript CG1983-RB
Escherichia coli b2951   UPF0001 family protein, PLP-binding
Echinococcus granulosus EgrG_001049210   proline synthetase co transcribed protein
Entamoeba histolytica EHI_188790   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_001049210   proline synthase co transcribed bacterial
Giardia lamblia GL50803_15041   Hypothetical protein, enzyme with a TIM-barrel fold
Homo sapiens ENSG00000147471   proline synthetase co-transcribed homolog (bacterial)
Leishmania braziliensis LbrM.23.1720   alanine racemase, putative;with=GeneDB:LmjF23.1480
Leishmania donovani LdBPK_231880.1   alanine racemase, putative
Leishmania infantum LinJ.23.1880   alanine racemase, putative;with=GeneDB:LmjF23.1480
Leishmania major LmjF.23.1480   alanine racemase, putative
Leishmania mexicana LmxM.23.1480   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_00735   hypothetical protein
Mycobacterium leprae ML0919   CONSERVED HYPOTHETICAL PROTEIN
Mus musculus ENSMUSG00000031485   proline synthetase co-transcribed
Mycobacterium tuberculosis Rv2148c   Conserved protein
Mycobacterium ulcerans MUL_3496   hypothetical protein
Neospora caninum NCLIV_010840   hypothetical protein
Oryza sativa 4337823   Os05g0150000
Onchocerca volvulus OVOC5074   Proline synthase homolog
Plasmodium berghei PBANKA_0820600   pyridoxal 5'-phosphate dependent enzyme class III, putative
Plasmodium falciparum PF3D7_0919700   pyridoxal 5'-phosphate dependent enzyme class III, putative
Plasmodium knowlesi PKNH_0717700   pyridoxal 5'-phosphate dependent enzyme class III, putative
Plasmodium vivax PVX_099400   hypothetical protein, conserved
Saccharomyces cerevisiae YBL036C   hypothetical protein
Schistosoma japonicum Sjp_0212560   ko:K06997 PROSC, LOC482854; proline synthetase co-transcribed homolog (bacterial), putative
Schistosoma mansoni Smp_070810   proline synthetase associated protein
Schmidtea mediterranea mk4.006372.00   Proline synthase co-transcribed bacterial homolog protein
Schmidtea mediterranea mk4.035922.03  
Trypanosoma brucei gambiense Tbg972.5.1770   hypothetical protein, conserved
Trypanosoma brucei Tb927.5.1280   alanine racemase, putative
Trypanosoma congolense TcIL3000_5_1300   alanine racemase, putative
Trypanosoma congolense TcIL3000_0_42700   alanine racemase, putative
Trypanosoma cruzi TcCLB.509767.90   alanine racemase, putative
Trypanosoma cruzi TcCLB.509601.90   alanine racemase, putative
Toxoplasma gondii TGME49_318720   pyridoxal phosphate enzyme, YggS family protein
Theileria parva TP02_0565   hypothetical protein, conserved
Trichomonas vaginalis TVAG_043550   proline synthetase associated protein, putative

Essentiality

LmjF.23.1480 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu2181 Mycobacterium tuberculosis non-essential nmpdr
Tb927.5.1280 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.5.1280 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.5.1280 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.5.1280 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b2951 Escherichia coli non-essential goodall
CELE_F09E5.8 Caenorhabditis elegans embryonic lethal wormbase
TGME49_318720 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
catalytic activity (GO:0003824) decreased (PATO:0000468) in vitro (MI:0492) inferred from specific protein inhibition (ECO:0000020) Leishmania amazonensis No drug identifiers listed for this gene.
Annotator: crowther@u.washington.edu. Comment: Drug: D-cycloserine. chemical inhibitors reduce alanine racemase activity. References: 16487314

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

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

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User comments

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Gene identifier LmjF.23.1480 (Leishmania major), alanine racemase, putative
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