Detailed view for LmjF.35.0700

Basic information

TDR Targets ID: 27494
Leishmania major, vacuolar ATP synthase subunit d, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 10.3432 | Length (AA): 276 | MW (Da): 30477 | 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

PF01813   ATP synthase subunit D

Gene Ontology

Mouse over links to read term descriptions.
GO:0042626   ATPase activity, coupled to transmembrane movement of substances  
GO:0015986   ATP synthesis coupled proton transport  

Metabolic Pathways

Oxidative phosphorylation (KEGG)
Global map (KEGG)
Phagosome (KEGG)

Structural information

Modbase 3D models:

There are 3 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
5 259 5d80 (G) 4 226 43.00 0 0.85 1.19471 0.86
10 242 5bw9 (G) 9 219 49.00 0 0.99 0.514803 2.33
156 253 4oyd (B) 12 111 15.00 0.87 0.02 0.481672 -0.3

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 60-80% 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_127301)

Species Accession Gene Product
Arabidopsis thaliana AT3G58730   V-type proton ATPase subunit D
Babesia bovis BBOV_III004650   V-type ATPase, D subunit family protein
Brugia malayi Bm1_13590   vacuolar ATP synthase subunit D
Candida albicans CaO19.10413   similar to S. cerevisiae VMA8 (YEL051W) vacuolar ATPase V1 domain subunit D
Candida albicans CaO19.2895   similar to S. cerevisiae VMA8 (YEL051W) vacuolar ATPase V1 domain subunit D
Caenorhabditis elegans CELE_F55H2.2   Protein VHA-14
Cryptosporidium hominis Chro.50340   vacuolar ATP synthase subunit D
Cryptosporidium parvum cgd5_530   vacuolar H-ATpase subunit D
Dictyostelium discoideum DDB_G0274331   vacuolar ATP synthase subunit D
Drosophila melanogaster Dmel_CG13167   Vacuolar H[+] ATPase 36kD subunit 2
Drosophila melanogaster Dmel_CG8186   Vacuolar H[+] ATPase 36kD subunit 1
Drosophila melanogaster Dmel_CG8310   Vacuolar H[+] ATPase 36kD subunit 3
Echinococcus granulosus EgrG_000413100   V type proton ATPase subunit D
Entamoeba histolytica EHI_056390   V-type ATPase, D subunit, putative
Echinococcus multilocularis EmuJ_000413100   V type proton ATPase subunit D
Giardia lamblia GL50803_3678   Vacuolar ATP synthase subunit D
Homo sapiens 51382   ATPase, H+ transporting, lysosomal 34kDa, V1 subunit D
Leishmania braziliensis LbrM.34.0690   vacuolar ATP synthase subunit d, putative
Leishmania donovani LdBPK_350710.1   vacuolar ATP synthase subunit d, putative
Leishmania infantum LinJ.35.0710   vacuolar ATP synthase subunit d, putative
Leishmania major LmjF.35.0700   vacuolar ATP synthase subunit d, putative
Leishmania mexicana LmxM.34.0700   vacuolar ATP synthase subunit d, putative
Loa Loa (eye worm) LOAG_07514   vacuolar ATP synthase subunit D
Mus musculus ENSMUSG00000021114   ATPase, H+ transporting, lysosomal V1 subunit D
Neospora caninum NCLIV_023610   vacuolar ATP synthase subunit d, putative
Oryza sativa 4337176   Os04g0643100
Plasmodium berghei PBANKA_1355000   V-type proton ATPase subunit D, putative
Plasmodium falciparum PF3D7_1341900   V-type proton ATPase subunit D, putative
Plasmodium knowlesi PKNH_1259500   V-type proton ATPase subunit D, putative
Plasmodium vivax PVX_082995   vacuolar ATP synthase subunit d, putative
Plasmodium yoelii PY03087   V-type ATPase, D subunit
Saccharomyces cerevisiae YEL051W   H(+)-transporting V1 sector ATPase subunit D
Schistosoma japonicum Sjp_0007070   ko:K02149 V-type H+-transporting ATPase subunit D, putative
Schistosoma mansoni Smp_103200   ATP synthase subunit d
Schmidtea mediterranea mk4.000818.00   V-type proton ATPase subunit D
Trypanosoma brucei gambiense Tbg972.10.4680   vacuolar ATP synthase subunit d, putative
Trypanosoma brucei Tb927.10.3760   vacuolar ATP synthase subunit d, putative
Trypanosoma congolense TcIL3000_10_3090   vacuolar ATP synthase subunit d, putative
Trypanosoma cruzi TcCLB.511001.190   vacuolar ATP synthase subunit d, putative
Trypanosoma cruzi TcCLB.509017.30   vacuolar ATP synthase subunit d
Toxoplasma gondii TGME49_281920   V-type ATPase, D subunit protein
Treponema pallidum TP0527   V-type ATPase, subunit D (atpD-2)
Theileria parva TP02_0488   vacuolar ATP synthase subunit D, putative
Trichomonas vaginalis TVAG_038640   ATP synthase subunit D, putative

Essentiality

LmjF.35.0700 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.3760 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.3760 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.3760 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.10.3760 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F55H2.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_F55H2.2 Caenorhabditis elegans larval arrest wormbase
CELE_F55H2.2 Caenorhabditis elegans sterile wormbase
TGME49_281920 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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

18 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.

User comments

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Gene identifier LmjF.35.0700 (Leishmania major), vacuolar ATP synthase subunit d, putative
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