Detailed view for LmjF.25.2140

Basic information

TDR Targets ID: 23809
Leishmania major, succinyl-CoA synthetase alpha subunit, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 9.4557 | Length (AA): 299 | MW (Da): 30912 | Paralog Number: 1

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

PF00549   CoA-ligase
PF02629   CoA binding domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0048037   cofactor binding  
GO:0005488   binding  
GO:0003824   catalytic activity  
GO:0008152   metabolic process  

Structural information

Modbase 3D models:

There are 2 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
3 299 2fp4 (A) 3 303 67.00 0 1 1.81 -1.74
2 299 2fp4 (A) 3 303 67.00 0 1 1.87836 -1.28

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_127106)

Species Accession Gene Product
Arabidopsis thaliana AT5G08300   Succinyl-CoA ligase [GDP-forming] subunit alpha-1
Arabidopsis thaliana AT5G23250   Succinyl-CoA ligase [GDP-forming] subunit alpha-2
Babesia bovis BBOV_III007780   succinyl-CoA synthetase, alpha subunit family protein
Brugia malayi Bm1_00350   succinyl-CoA ligase [GDP-forming] alpha-chain, mitochindrial
Candida albicans CaO19.3358   succinate-CoA ligase
Candida albicans CaO19.10866   succinate-CoA ligase
Caenorhabditis elegans CELE_F23H11.3   Protein SUCL-2
Caenorhabditis elegans CELE_C05G5.4   Protein SUCL-1
Chlamydia trachomatis CT_822   succinyl-CoA ligase subunit alpha
Dictyostelium discoideum DDB_G0289325   GTP-specific succinyl-CoA synthetase alpha subunit
Drosophila melanogaster Dmel_CG6255   CG6255 gene product from transcript CG6255-RA
Drosophila melanogaster Dmel_CG1065   Succinyl coenzyme A synthetase alpha subunit
Escherichia coli b0729   succinyl-CoA synthetase, NAD(P)-binding, alpha subunit
Echinococcus granulosus EgrG_001199000   succinyl coenzyme A synthetase alpha subunit
Echinococcus multilocularis EmuJ_001199000   succinyl coenzyme A synthetase alpha subunit
Homo sapiens ENSG00000163541   succinate-CoA ligase, alpha subunit
Leishmania braziliensis LbrM.25.1710   succinyl-CoA synthetase alpha subunit, putative
Leishmania braziliensis LbrM.25.1700   succinyl-CoA synthetase alpha subunit, putative
Leishmania donovani LdBPK_252220.1   succinyl-CoA synthetase alpha subunit, putative
Leishmania infantum LinJ.25.2230   succinyl-CoA synthetase alpha subunit, putative
Leishmania major LmjF.25.2140   succinyl-CoA synthetase alpha subunit, putative
Leishmania major LmjF.25.2130   succinyl-CoA synthetase alpha subunit, putative
Leishmania mexicana LmxM.25.2140   succinyl-CoA synthetase alpha subunit, putative
Leishmania mexicana LmxM.25.2130   succinyl-CoA synthetase alpha subunit, putative
Loa Loa (eye worm) LOAG_11959   hypothetical protein
Loa Loa (eye worm) LOAG_07230   succinate-CoA ligase
Mycobacterium leprae ML0156   Probable succinyl-CoA synthetase (alpha chain) SucD (SCS-alpha)
Mus musculus ENSMUSG00000052738   succinate-CoA ligase, GDP-forming, alpha subunit
Mycobacterium tuberculosis Rv0952   Probable succinyl-CoA synthetase (alpha chain) SucD (SCS-alpha)
Mycobacterium ulcerans MUL_4719   succinyl-CoA synthetase subunit alpha
Neospora caninum NCLIV_042590   2-oxoglutarate dehydrogenase E1 component, related
Oryza sativa 4343710   Os07g0577700
Onchocerca volvulus OVOC5451  
Plasmodium berghei PBANKA_0938500   succinyl-CoA synthetase alpha subunit, putative
Plasmodium falciparum PF3D7_1108500   succinyl-CoA synthetase alpha subunit, putative
Plasmodium knowlesi PKNH_0906100   succinyl-CoA synthetase alpha subunit, putative
Plasmodium vivax PVX_091100   succinyl-CoA synthetase alpha subunit, putative
Plasmodium yoelii PY05049   Succinyl-CoA synthetase alpha subunit
Saccharomyces cerevisiae YOR142W   succinate--CoA ligase (GDP-forming) subunit alpha
Schistosoma japonicum Sjp_0303530   ko:K01899 succinate--CoA ligase (GDP-forming) alpha chain [EC6.2.1.4A], putative
Schistosoma mansoni Smp_052060   succinyl-CoA synthetase-related
Schmidtea mediterranea mk4.000163.09   Succinyl-CoA ligase
Schmidtea mediterranea mk4.058520.01  
Trypanosoma brucei gambiense Tbg972.3.2200   succinyl-CoA synthetase alpha subunit, putative
Trypanosoma brucei Tb927.3.2230   succinyl-CoA synthetase alpha subunit, putative
Trypanosoma congolense TcIL3000_3_1350   succinyl-CoA synthetase alpha subunit, putative
Trypanosoma cruzi TcCLB.508479.340   succinyl-CoA synthetase alpha subunit, putative
Toxoplasma gondii TGME49_290600   succinyl-CoA-synthetase alpha SCSA
Theileria parva TP04_0660   succinyl-CoA synthetase, alpha subunit, putative
Trichomonas vaginalis TVAG_318670   succinate thiokinase a subunit
Trichomonas vaginalis TVAG_047890   succinate thiokinase a subunit
Trichomonas vaginalis TVAG_165340   succinate thiokinase a subunit
Wolbachia endosymbiont of Brugia malayi Wbm0519   succinyl-CoA synthetase, alpha subunit

Essentiality

LmjF.25.2140 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu967 Mycobacterium tuberculosis essential nmpdr
Tb927.3.2230 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.3.2230 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.3.2230 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.3.2230 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b0729 Escherichia coli non-essential goodall
CELE_C05G5.4 Caenorhabditis elegans embryonic lethal wormbase
CELE_F23H11.3 Caenorhabditis elegans embryonic lethal wormbase
PBANKA_0938500 Plasmodium berghei Slow plasmo
TGME49_290600 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • 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
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

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): 0.3

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 Succinic Thiokinase (6.2.1.4 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

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

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Gene identifier LmjF.25.2140 (Leishmania major), succinyl-CoA synthetase alpha subunit, putative
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