Detailed view for LmjF.36.3810

Basic information

TDR Targets ID: 26658
Leishmania major, glycine synthase, putative;with=GeneDB:LinJ36_V3.4000
Source Database / ID:  TriTrypDB  GeneDB

pI: 9.0651 | Length (AA): 377 | MW (Da): 41331 | Paralog Number: 1

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

PF01571   Aminomethyltransferase folate-binding domain
PF08669   Glycine cleavage T-protein C-terminal barrel domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005737   cytoplasm  
GO:0005515   protein binding  
GO:0004047   aminomethyltransferase activity  
GO:0006546   glycine catabolic process  

Structural information

Modbase 3D models:

There are 4 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
3 375 1x31 (A) 571 962 23.00 0 1 1.3 -0.64
5 374 1wsr (A) 5 373 43.00 0 1 1.59 -1.1
3 374 1pj5 (A) 428 827 24.00 0 1 1.18644 0.22
5 374 1wsr (A) 5 373 43.00 0 1 1.50263 -0.42

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. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Lower 0-20% 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_127412)

Species Accession Gene Product
Arabidopsis thaliana AT1G11860   aminomethyltransferase
Candida albicans CaO19.12965   T subunit of glycine decarboxylase
Candida albicans CaO19.5519   glycine decarboxylase T subunit
Caenorhabditis elegans CELE_F25B4.1   Protein GCST-1
Dictyostelium discoideum DDB_G0292326   glycine cleavage system T-protein
Drosophila melanogaster Dmel_CG6415   CG6415 gene product from transcript CG6415-RA
Escherichia coli b2905   aminomethyltransferase, tetrahydrofolate-dependent, subunit (T protein) of glycine cleavage complex
Homo sapiens ENSG00000145020   aminomethyltransferase
Leishmania braziliensis LbrM.35.4040   aminomethyltransferase, mitochondrial precursor, putative
Leishmania donovani LdBPK_364000.1   aminomethyltransferase, mitochondrial, putative
Leishmania infantum LinJ.36.4000   glycine synthase, putative
Leishmania infantum LinJ.36.3990   glycine synthase, putative
Leishmania major LmjF.36.3800   glycine synthase, putative;with=GeneDB:LinJ36_V3.3990
Leishmania major LmjF.36.3810   glycine synthase, putative;with=GeneDB:LinJ36_V3.4000
Leishmania mexicana LmxM.36.3810   aminomethyltransferase, mitochondrial precursor, putative
Leishmania mexicana LmxM.36.3800   aminomethyltransferase, mitochondrial precursor, putative
Mycobacterium leprae ML0865   Probable aminomethyltransferase GcvT (Glycine cleavage system T protein)
Mus musculus 434437   aminomethyltransferase
Mycobacterium tuberculosis Rv2211c   Probable aminomethyltransferase GcvT (glycine cleavage system T protein)
Mycobacterium ulcerans MUL_3571   glycine cleavage system aminomethyltransferase T
Neospora caninum NCLIV_051210   aminomethyltransferase, mitochondrial, putative
Oryza sativa 4337051   Os04g0623800
Plasmodium berghei PBANKA_1141300   aminomethyltransferase, mitochondrial
Plasmodium falciparum PF3D7_1365500   aminomethyltransferase, mitochondrial, putative
Plasmodium knowlesi PKNH_1105800   aminomethyltransferase, mitochondrial, putative
Plasmodium vivax PVX_115235   glycine cleavage system T protein, putative
Plasmodium yoelii PY02845   aminomethyltransferase, mitochondrial precursor
Saccharomyces cerevisiae YDR019C   glycine decarboxylase subunit T
Schistosoma japonicum Sjp_0113850   ko:K00605 aminomethyltransferase [EC2.1.2.10], putative
Schistosoma japonicum Sjp_0306400   Aminomethyltransferase, mitochondrial precursor, putative
Schistosoma mansoni Smp_128980   aminomethyltransferase
Schmidtea mediterranea mk4.005726.01   Aminomethyltransferase, mitochondrial
Schmidtea mediterranea mk4.027093.00   Aminomethyltransferase
Schmidtea mediterranea mk4.077281.00  
Schmidtea mediterranea mk4.063202.01   Aminomethyltransferase, mitochondrial
Schmidtea mediterranea mk4.016905.00   Aminomethyltransferase, mitochondrial
Trypanosoma brucei gambiense Tbg972.11.10860   aminomethyltransferase, putative
Trypanosoma brucei Tb927.11.9670   aminomethyltransferase, mitochondrial, putative
Trypanosoma congolense TcIL3000.11.10170   aminomethyltransferase, mitochondrial, putative
Trypanosoma cruzi TcCLB.504017.40   aminomethyltransferase, mitochondrial, putative
Trypanosoma cruzi TcCLB.511231.50   aminomethyltransferase, mitochondrial, putative
Toxoplasma gondii TGME49_237470   glycine cleavage T-protein (aminomethyl transferase) domain-containing protein

Essentiality

LmjF.36.3810 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.1440 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.1440 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.1440 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.1440 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b2905 Escherichia coli non-essential goodall
PBANKA_1141300 Plasmodium berghei Dispensable plasmo
TGME49_237470 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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
  • 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.
  • 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
  • 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.
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

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

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

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier LmjF.36.3810 (Leishmania major), glycine synthase, putative;with=GeneDB:LinJ36_V3.4000
Title for this comment
Comment