Detailed view for LmjF.15.1020

Basic information

TDR Targets ID: 26175
Leishmania major, solanesyl-diphosphate synthase, putative

Source Database / ID:  TriTrypDB  GeneDB

pI: 6.3147 | Length (AA): 359 | MW (Da): 39138 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG3

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

PF00348   Polyprenyl synthetase

Gene Ontology

Mouse over links to read term descriptions.
GO:0008299   isoprenoid biosynthetic process  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

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
11 359 1uby () 22 367 18.00 0 1 1.12 -0.73
28 358 1wy0 (A) 8 341 31.00 0 1 1.33 -1.34
18 357 4lob (A) 0 323 30.00 0 1 1.22958 -0.31
23 359 3oyr (B) 13 335 28.00 0 1 1.28722 -0.77
28 358 3aq0 (A) 11 347 37.00 0 1 1.30841 -0.59
28 274 5e8l (A) 13 269 28.00 0 0.77 0.875422 -0.13
113 282 4lls (A) 66 247 39.00 0 0.52 0.643238 0.54

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
Mid 40-60% 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_126937)

Species Accession Gene Product
Arabidopsis thaliana AT1G17050   solanesyl diphosphate synthase 2
Arabidopsis thaliana AT1G78510   solanesyl diphosphate synthase 1
Arabidopsis thaliana AT2G34630   geranyl diphosphate synthase 1
Babesia bovis BBOV_IV007310   polyprenyl synthetase superfamily protein
Brugia malayi Bm1_35720   Polyprenyl synthetase family protein
Candida albicans CaO19.7478   trans-hexaprenyltranstransferase
Caenorhabditis elegans CELE_C24A11.9   Protein COQ-1
Cryptosporidium hominis Chro.70416   hypothetical protein
Cryptosporidium parvum cgd7_3730   long chain fatty acyl diphosphate synthase
Dictyostelium discoideum DDB_G0280293   hexaprenyl pyrophosphate synthetase
Drosophila melanogaster Dmel_CG31005   CG31005 gene product from transcript CG31005-RA
Escherichia coli b3187   octaprenyl diphosphate synthase
Echinococcus granulosus EgrG_000256100   decaprenyl diphosphate synthase subunit 1
Entamoeba histolytica EHI_028880   geranylgeranyl pyrophosphate synthetase, putative
Entamoeba histolytica EHI_105060   geranylgeranyl pyrophosphate synthase, putative
Echinococcus multilocularis EmuJ_000256100   decaprenyl diphosphate synthase subunit 1
Homo sapiens ENSG00000148459   prenyl (decaprenyl) diphosphate synthase, subunit 1
Leishmania braziliensis LbrM.15.1060   solanesyl-diphosphate synthase, putative
Leishmania donovani LdBPK_151080.1   solanesyl-diphosphate synthase, putative
Leishmania infantum LinJ.15.1080   solanesyl-diphosphate synthase, putative
Leishmania major LmjF.15.1020   solanesyl-diphosphate synthase, putative
Leishmania mexicana LmxM.15.1020   farnesyl synthetase, putative
Loa Loa (eye worm) LOAG_00347   polyprenyl synthetase
Mycobacterium leprae ML2277   PROBABLE POLYPRENYL-DIPHOSPHATE SYNTHASE GRCC1 (POLYPRENYL PYROPHOSPHATE SYNTHETASE)
Mus musculus ENSMUSG00000026784   prenyl (solanesyl) diphosphate synthase, subunit 1
Mycobacterium tuberculosis Rv0562   Probable polyprenyl-diphosphate synthase GrcC1 (polyprenyl pyrophosphate synthetase)
Mycobacterium ulcerans MUL_0664   polyprenyl diphosphate synthetase, GrcC1
Neospora caninum NCLIV_036980   hypothetical protein
Oryza sativa 9272514   Os08g0193100
Oryza sativa 4351957   Os12g0271700
Oryza sativa 4341844   Os06g0678200
Plasmodium berghei PBANKA_0300800   octaprenyl pyrophosphate synthase, putative
Plasmodium falciparum PF3D7_0202700   octaprenyl pyrophosphate synthase
Plasmodium knowlesi PKNH_0418400   octaprenyl pyrophosphate synthase, putative
Plasmodium vivax PVX_003575   octaprenyl pyrophosphate synthase, putative
Plasmodium yoelii PY00446   Polyprenyl synthetase, putative
Saccharomyces cerevisiae YBR003W   trans-hexaprenyltranstransferase
Schistosoma japonicum Sjp_0306360   Decaprenyl-diphosphate synthase subunit 1, putative
Schistosoma japonicum Sjp_0071520   ko:K00810 similar to prenyl diphosphate synthase, subunit 1 [EC:2.5.1.-], putative
Schistosoma mansoni Smp_059800   trans-prenyltransferase
Schmidtea mediterranea mk4.001177.03  
Schmidtea mediterranea mk4.001177.02   Prenyl transferase
Trypanosoma brucei gambiense Tbg972.9.3090   farnesyl pyrophosphate synthetase, putative
Trypanosoma brucei Tb927.9.5890   solanesyl-diphosphate synthase, putative
Trypanosoma cruzi TcCLB.509445.30   solanesyl-diphosphate synthase
Trypanosoma cruzi TcCLB.427091.10   solanesyl-diphosphate synthase, putative
Trypanosoma cruzi TcCLB.422031.10   solanesyl-diphosphate synthase, putative
Toxoplasma gondii TGME49_269430   polyprenyl synthetase superfamily protein
Theileria parva TP03_0238   prenyl transferase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0532   geranylgeranyl pyrophosphate synthase

Essentiality

LmjF.15.1020 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.160.4300 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.160.4300 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.160.4300 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.160.4300 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b3187 Escherichia coli essential goodall
CELE_C24A11.9 Caenorhabditis elegans slow growth wormbase
PBANKA_0300800 Plasmodium berghei Essential plasmo
TGME49_269430 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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

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): 0.4


Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Trypanosoma cruzi solanesyl-diphosphate synthase, putative Compounds References
Trypanosoma cruzi solanesyl-diphosphate synthase, putative Compounds References
Trypanosoma cruzi solanesyl-diphosphate synthase Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets

Obtained from network model

Ranking Plot


Putative Drugs List


Compound Raw Global Species
0.1486 0.3458 0.4425
0.1054 0.4087 0.4868
0.0445 0.2829 0.2829
0.0429 0.451 0.2971
0.0398 0.2674 0.1176
0.0189 0.4012 0.3977
0.0189 0.4012 0.3977
0.0191 0.3456 0.336
0.0447 0.2832 0.2829
0.0824 0.358 0.2656
0.084 0.2579 0.255
0.0411 0.2525 0.2784
0.3926 0.2756 0.2756
0.3926 0.2756 0.2756
0.0433 0.267 0.2596
0.0425 0.2773 0.2024
0.1059 0.5002 0.4886
0.1685 0.2666 0.2666
0.047 0.2506 0
0.9267 0.3083 0.3083
0.0411 0.2525 0.2784
0.0663 0.273 0.2716
0.0169 0.3173 0.2587
0.1054 0.4087 0.4868
0.0448 0.2646 0.1532
0.4173 0.2761 0.276
0.1054 0.4087 0.4868
0.0327 0.2716 0.2714
0.0663 0.273 0.2716
0.1059 0.5002 0.4886
0.0411 0.2525 0.2784
0.0096429 0.366433 0.366433
0.0157 0.5396 0.4371
0.9267 0.3083 0.3083
0.0157 0.3438 0.3438
0.0679 0.2583 0.2573
0.1054 0.4087 0.4868
0.0667 0.4405 0.4403
0.0667 0.4405 0.4403
0.0774 0.2668 0.2668
0.1821 0.2575 0.257
0.0157 0.3438 0.3438
0.1063 0.2647 0.2647
0.0128 0.288 0.0095
0.0118 0.3145 0.2761
0.0679 0.2583 0.2573
0.2036 0.3184 0.1474
0.0953 0.2702 0.2691
0.0157 0.3438 0.3438
0.0679 0.2583 0.2573
0.1059 0.5002 0.4886
0.1054 0.4087 0.4868
0.084 0.2579 0.255
0.0706 0.2737 0.272
0.0261 0.2812 0.2877
0.1063 0.2647 0.2647
0.1374 0.2627 0.2627
0.05 0.2528 0.2528
0.9267 0.3083 0.3083
0.061 0.2693 0.262
0.0824 0.358 0.2656
0.0425 0.2773 0.2024
0.0517 0.2702 0
0.0667 0.4405 0.4403
0.1059 0.5002 0.4886
0.1059 0.5002 0.4886
0.0157 0.5529 0.5529
0.0673 0.2639 0.2622
0.0788 0.2789 0.228
0.026 0.2585 0.2565
0.0332 0.2653 0.2653
0.0704 0.3928 0.3922
0.0433 0.267 0.2596
0.1054 0.4087 0.4868
0.0679 0.2583 0.2573
0.0157 0.3438 0.3438
0.0416 0.3269 0.2983
0.026 0.2585 0.2565
0.0425 0.2654 0.1385
0.0583 0.3069 0.3067
0.4054 0.2847 0.2847
0.0545 0.2666 0
0.0157 0.3438 0.3438
0.0519 0.2681 0.2552
0.0494 0.29 0.264
0.0824 0.358 0.2656
0.1648 0.4301 0.427
0.0635 0.2606 0.2343
0.0377 0.2905 0.145
0.0679 0.2583 0.2573
0.1054 0.4087 0.4868
0.1054 0.4087 0.4868
0.1171 0.3221 0.2788
0.0824 0.358 0.2656
0.0436 0.3099 0.3037
0.8288 0.3209 0.3209
0.0254 0.2727 0.2717

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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Gene identifier LmjF.15.1020 (Leishmania major), solanesyl-diphosphate synthase, putative
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