Detailed view for LmjF.35.2120

Basic information

TDR Targets ID: 25884
Leishmania major, R-SNARE protein, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.8487 | Length (AA): 205 | MW (Da): 23042 | 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

PF00957   Synaptobrevin

Gene Ontology

Mouse over links to read term descriptions.
GO:0016021   integral to membrane  
GO:0016192   vesicle-mediated transport  
GO:0006810   transport  

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
1 143 1h8m (A) 1 139 24.00 0 0.99 1.14 -1.29
2 136 1ifq (A) 1 126 10.00 0 0.51 0.77 -1.7
144 197 1gl2 (A) 11 64 28.00 0.0000000095 0.01 0.66 -1.52
1 139 3bw6 (A) 1 135 25.00 0 1 1.09485 -1.09
1 198 3kyq (A) 1 192 36.00 0 1 1.49515 -1.05

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_127692)

Species Accession Gene Product
Arabidopsis thaliana AT5G58060   VAMP-like protein YKT61
Arabidopsis thaliana AT5G58180   VAMP-like protein YKT62
Babesia bovis BBOV_I000460   conserved hypothetical protein
Brugia malayi Bm1_22895   Synaptobrevin homolog YKT6
Candida albicans CaO19.10491   similar to S. cerevisiae VKT6 (YKL196C) synaptobrevin v-SNARE protein, ER_Golgi transport
Candida albicans CaO19.2974   similar to S. cerevisiae VKT6 (YKL196C) synaptobrevin v-SNARE protein, ER_Golgi transport
Caenorhabditis elegans CELE_B0361.10   Protein YKT-6
Cryptosporidium hominis Chro.60069   hypothetical protein
Cryptosporidium parvum cgd6_510   synaptobrevin/VAMP-like protein
Dictyostelium discoideum DDB_G0291656   longin domain-containing protein
Drosophila melanogaster Dmel_CG1515   YKT6 ortholog (S. cerevisiae)
Echinococcus granulosus EgrG_000826400   synaptobrevin YKT6
Entamoeba histolytica EHI_052110   hypothetical protein
Entamoeba histolytica EHI_037810   hypothetical protein
Echinococcus multilocularis EmuJ_000826400   synaptobrevin YKT6
Giardia lamblia GL50803_7306   Prenylated synaptobrevin/VAMP, putative
Homo sapiens ENSG00000106636   YKT6 v-SNARE homolog (S. cerevisiae)
Leishmania braziliensis LbrM.34.2040   vesicle-associated membrane protein, putative
Leishmania donovani LdBPK_352150.1   vesicle-associated membrane protein, putative
Leishmania infantum LinJ.35.2150   vesicle-associated membrane protein, putative
Leishmania major LmjF.35.2120   R-SNARE protein, putative
Leishmania mexicana LmxM.34.2120   R-SNARE protein, putative
Loa Loa (eye worm) LOAG_05680   hypothetical protein
Mus musculus ENSMUSG00000002741   YKT6 homolog (S. Cerevisiae)
Neospora caninum NCLIV_052340   hypothetical protein
Oryza sativa 4324461   Os01g0964000
Oryza sativa 4325070   Os01g0866300
Plasmodium berghei PBANKA_1339900   SNARE protein, putative
Plasmodium falciparum PF3D7_1324700   SNARE protein, putative
Plasmodium knowlesi PKNH_1204100   snare protein homologue, putative
Plasmodium yoelii PY03887   hypothetical protein
Saccharomyces cerevisiae YKL196C   palmitoyltransferase YKT6
Schistosoma japonicum Sjp_0305550   ko:K08516 synaptobrevin homolog YKT6, putative
Schistosoma mansoni Smp_047450   snare protein ykt6
Schmidtea mediterranea mk4.004767.01   Putative snare protein ykt6
Trypanosoma brucei gambiense Tbg972.9.8790   vesicle-associated membrane protein, putative
Trypanosoma brucei Tb927.9.14080   vesicle-associated membrane protein, putative
Trypanosoma cruzi TcCLB.506999.150   vesicle-associated membrane protein, putative
Trypanosoma cruzi TcCLB.510759.60   vesicle-associated membrane protein, putative
Toxoplasma gondii TGME49_215420   SNARE protein
Theileria parva TP02_0923   hypothetical protein
Trichomonas vaginalis TVAG_432570   snare protein ykt6, putative

Essentiality

LmjF.35.2120 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.4610 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb09.211.4610 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.211.4610 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.211.4610 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_B0361.10 Caenorhabditis elegans embryonic lethal wormbase
CELE_B0361.10 Caenorhabditis elegans larval arrest wormbase
CELE_B0361.10 Caenorhabditis elegans slow growth wormbase
CELE_B0361.10 Caenorhabditis elegans sterile wormbase
YKL196C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1339900 Plasmodium berghei Essential plasmo
TGME49_215420 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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

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.

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User comments

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Gene identifier LmjF.35.2120 (Leishmania major), R-SNARE protein, putative
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