Detailed view for LmjF.35.4720

Basic information

TDR Targets ID: 22403
Leishmania major, lipoic acid containing carrier protein, putative;with=GeneDB:LinJ35_V3.4790
Source Database / ID:  TriTrypDB  GeneDB

pI: 4.053 | Length (AA): 107 | MW (Da): 11666 | 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

PF01597   Glycine cleavage H-protein

Gene Ontology

Mouse over links to read term descriptions.
GO:0019464   glycine decarboxylation via glycine cleavage system  
GO:0005960   glycine cleavage complex  
GO:0005739   mitochondrion  
GO:0006546   glycine catabolic process  

Structural information

Modbase 3D models:

There are 7 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
2 107 1onl (A) 18 125 42.00 0 1 1.42 -0.6
2 107 1htp () 18 125 46.00 0 1 1.48 -0.69
2 107 1zko (A) 15 122 47.00 0 1 1.49 -0.64
2 107 1hpc (A) 18 125 46.00 0 1 1.65255 -1.18
2 107 3a7l (A) 19 126 46.00 0 1 1.64635 -1.14
3 107 2edg (A) 20 126 52.00 0 1 1.66721 -0.82
4 107 1onl (A) 20 125 43.00 0 1 1.58446 -1.2

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_127169)

Species Accession Gene Product
Arabidopsis thaliana AT1G32470   probable glycine cleavage system H protein 2
Arabidopsis thaliana AT2G35120   glycine cleavage system H protein 2
Arabidopsis thaliana AT2G35370   glycine decarboxylase complex protein H
Brugia malayi Bm1_19690   glycine cleavage system H protein
Candida albicans CaO19.12473   H-protein subunit of glycine cleavage system
Candida albicans CaO19.5006   H-protein subunit of glycine cleavage system
Caenorhabditis elegans CELE_D1025.2   Protein GCSH-1
Caenorhabditis elegans CELE_F52A8.5   Protein F52A8.5
Chlamydia trachomatis CT_282   glycine cleavage system protein H
Dictyostelium discoideum DDB_G0287791   glycine cleavage system H-protein
Dictyostelium discoideum DDB_G0290845   glycine cleavage system H-protein
Dictyostelium discoideum DDB_G0287773   glycine cleavage system H-protein
Drosophila melanogaster Dmel_CG7758   pumpless
Escherichia coli b2904   glycine cleavage complex lipoylprotein
Echinococcus granulosus EgrG_000694900   glycine cleavage system H protein
Echinococcus multilocularis EmuJ_000694900   glycine cleavage system H protein
Homo sapiens 101060817   glycine cleavage system H protein, mitochondrial-like
Homo sapiens ENSG00000140905   glycine cleavage system protein H (aminomethyl carrier)
Leishmania braziliensis LbrM.34.4690   glycine cleavage system H protein, putative
Leishmania donovani LdBPK_354790.1   glycine cleavage system H protein, putative
Leishmania infantum LinJ.35.4790   lipoic acid containing carrier protein, putative
Leishmania major LmjF.35.4720   lipoic acid containing carrier protein, putative;with=GeneDB:LinJ35_V3.4790
Leishmania mexicana LmxM.34.4720   glycine cleavage system H protein, putative
Loa Loa (eye worm) LOAG_10305   glycine cleavage system H protein
Mycobacterium leprae ML2077c   PROBABLE GLYCINE CLEAVAGE SYSTEM H PROTEIN GCVH
Mus musculus ENSMUSG00000034424   glycine cleavage system protein H (aminomethyl carrier)
Mus musculus 102641654   glycine cleavage system H protein, mitochondrial-like
Mycobacterium tuberculosis Rv1826   Probable glycine cleavage system H protein GcvH
Mycobacterium ulcerans MUL_3045   glycine cleavage system protein H
Mycobacterium ulcerans MUL_4903   glycine cleavage system H protein GcvH
Neospora caninum NCLIV_021960   Glycine cleavage system H protein, mitochondrial (Precursor), related
Oryza sativa 4349114   Os10g0516100
Oryza sativa 9269154   Os02g0169700
Oryza sativa 4328441   Os02g0170100
Oryza sativa 4341790   Os06g0667600
Onchocerca volvulus OVOC11752   Glycine cleavage system H protein, mitochondrial homolog
Plasmodium berghei PBANKA_0915500   glycine cleavage system H protein, putative
Plasmodium falciparum PF3D7_1132900   glycine cleavage system H protein
Plasmodium knowlesi PKNH_0931100   glycine cleavage system H protein, putative
Plasmodium vivax PVX_092250   glycine cleavage system H protein, putative
Plasmodium yoelii PY05949   probable glycine cleavage system h protein
Saccharomyces cerevisiae YAL044C   glycine decarboxylase subunit H
Schistosoma japonicum Sjp_0066200   ko:K02437 glycine cleavage system H protein, putative
Schmidtea mediterranea mk4.027782.01   Glycine cleavage system H protein, mitochondrial
Schmidtea mediterranea mk4.018963.03   Glycine cleavage system H protein, mitochondrial
Trypanosoma brucei gambiense Tbg972.9.5660   glycine cleavage system H protein, putative
Trypanosoma brucei Tb927.9.9840   lipoic acid containing carrier protein, putative
Trypanosoma cruzi TcCLB.508457.30   lipoic acid containing carrier protein, putative
Trypanosoma cruzi TcCLB.506885.430   lipoic acid containing carrier protein, putative
Toxoplasma gondii TGME49_202960   glycine cleavage H-protein
Trichomonas vaginalis TVAG_177600   glycine cleavage system H protein, putative
Trichomonas vaginalis TVAG_100550   glycine cleavage system H protein, putative

Essentiality

LmjF.35.4720 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.1380 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.211.1380 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb09.211.1380 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb09.211.1380 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b2904 Escherichia coli non-essential goodall
CELE_F52A8.5 Caenorhabditis elegans embryonic lethal wormbase
PBANKA_0915500 Plasmodium berghei Essential plasmo
TGME49_202960 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.
  • 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
  • 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
  • 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
  • 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
  • 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

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

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

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.35.4720 (Leishmania major), lipoic acid containing carrier protein, putative;with=GeneDB:LinJ35_V3.4790
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