Detailed view for TP0603

Basic information

TDR Targets ID: 596628
Treponema pallidum, undecaprenyl pyrophosphate synthase
Source Database / ID:  KEGG  

pI: 8.6151 | Length (AA): 228 | MW (Da): 26270 | 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

PF01255   Putative undecaprenyl diphosphate synthase

Gene Ontology

Mouse over links to read term descriptions.
GO:0016765   transferase activity, transferring alkyl or aryl (other than methyl) groups  

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
1 225 2d2r (B) 5 230 43.00 0 1 1.47744 -0.79
2 226 2vg3 (A) 69 295 40.00 0 1 1.57924 -1.27
2 227 4h8e (A) 26 253 39.00 0 1 1.58883 -1.16

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_126777)

Species Accession Gene Product
Arabidopsis thaliana AT5G60500   dehydrodolichyl diphosphate synthase 7
Arabidopsis thaliana AT5G58780   Z,E-mixed heptaprenyl diphosphate synthase
Arabidopsis thaliana AT5G60510   cis-prenyltransferase 9
Arabidopsis thaliana AT2G17570   cis-prenyltransferase 1
Arabidopsis thaliana AT2G23410   cis-prenyltransferase
Arabidopsis thaliana AT5G58770   dehydrodolichyl diphosphate synthase 2
Arabidopsis thaliana AT2G23400   undecaprenyl pyrophosphate synthetase family protein
Arabidopsis thaliana AT5G58782   dehydrodolichyl diphosphate synthase 4
Arabidopsis thaliana AT5G58784   dehydrodolichyl diphosphate synthase 5
Babesia bovis BBOV_IV002310   undecaprenyl pyrophosphate synthetase, putative
Brugia malayi Bm1_28770   Undecaprenyl diphosphate synthase family protein
Candida albicans CaO19.4028   Cis-prenyltransferase
Candida albicans CaO19.11511   Cis-prenyltransferase
Candida albicans CaO19.12700   cis-prenyltransferase-like orf
Candida albicans CaO19.5236   cis-prenyltransferase-like orf
Caenorhabditis elegans CELE_T01G1.4   Protein T01G1.4
Cryptosporidium parvum cgd4_1510   conserved hypothetical protein
Chlamydia trachomatis CT_450   isoprenyl transferase
Dictyostelium discoideum DDB_G0291436   hypothetical protein
Drosophila melanogaster Dmel_CG10778   CG10778 gene product from transcript CG10778-RB
Escherichia coli b0174   undecaprenyl pyrophosphate synthase
Echinococcus granulosus EgrG_000132300   dehydrodolichyl diphosphate synthase
Echinococcus multilocularis EmuJ_000132300   dehydrodolichyl diphosphate synthase
Giardia lamblia GL50803_15256   Undecaprenyl pyrophosphate synthase
Homo sapiens ENSG00000117682   dehydrodolichyl diphosphate synthase
Leishmania braziliensis LbrM.13.0020   cis-prenyltransferase-like protein
Leishmania donovani LdBPK_130020.1   cis-prenyltransferase-like protein
Leishmania infantum LinJ.13.0020   cis-prenyltransferase-like protein
Leishmania major LmjF.13.0020   cis-prenyltransferase-like protein
Leishmania mexicana LmxM.13.0020   cis-prenyltransferase-like protein
Loa Loa (eye worm) LOAG_02395   hypothetical protein
Mycobacterium leprae ML2467   SHORT (C15) CHAIN Z-ISOPRENYL DIPHOSPHATE SYNTHASE (Z-FPP SYNTHASE) (Z-FARNESYL DIPHOSPHATE SYNTHASE) (Z-FPP SYNTHETASE) (Z-FARN
Mycobacterium leprae ML0634   Probable Long (C50) chain Z-isoprenyl diphosphate synthase (Z-DECAPRENYL DIPHOSPHATE SYNTHASE)
Mus musculus ENSMUSG00000012117   dehydrodolichyl diphosphate synthase
Mycobacterium tuberculosis Rv1086   Short (C15) chain Z-isoprenyl diphosphate synthase (Z-FPP synthase) (Z-farnesyl diphosphate synthase) (Z-FPP synthetase) (Z-farn
Mycobacterium tuberculosis Rv2361c   Long (C50) chain Z-isoprenyl diphosphate synthase (Z-decaprenyl diphosphate synthase)
Mycobacterium ulcerans MUL_3614   undecaprenyl pyrophosphate synthase
Mycobacterium ulcerans MUL_0193   short (C15) chain Z-isoprenyl diphosphate synthase, UppS
Mycobacterium ulcerans MUL_3171   Z-decaprenyl diphosphate synthase
Neospora caninum NCLIV_059180   GF20994, related
Oryza sativa 4324755   Os01g0857200
Oryza sativa 4340251   Os06g0167400
Oryza sativa 4343863   Os07g0607700
Onchocerca volvulus OVOC2159   Dehydrodolichyl diphosphate synthase homolog
Plasmodium berghei PBANKA_0704200   dehydrodolichyl diphosphate synthetase, putative
Plasmodium falciparum PF3D7_0826400   dehydrodolichyl diphosphate synthetase, putative
Plasmodium knowlesi PKNH_1320600   dehydrodolichyl diphosphate synthetase, putative
Plasmodium vivax PVX_089040   dehydrodolichyl diphosphate synthetase, putative
Plasmodium yoelii PY05575   undecaprenyl pyrophosphate synthetase-like-related
Plasmodium yoelii PY05574   hypothetical protein
Saccharomyces cerevisiae YBR002C   Rer2p
Saccharomyces cerevisiae YMR101C   Srt1p
Schistosoma japonicum Sjp_0052490   ko:K00810 dehydrodolichyl diphosphate synthase [EC:2.5.1.-], putative
Schistosoma mansoni Smp_048520.2   dehydrodolichyl diphosphate synthase (dedol-pp synthase)
Schistosoma mansoni Smp_048520.1   dehydrodolichyl diphosphate synthase (dedol-pp synthase)
Schistosoma mansoni Smp_048520.3   dehydrodolichyl diphosphate synthase (dedol-pp synthase)
Schmidtea mediterranea mk4.007105.00   Dehydrodolichyl diphosphate synthase
Schmidtea mediterranea mk4.021140.01   Dehydrodolichyl diphosphate synthase
Trypanosoma brucei gambiense Tbg972.7.6850   cis-prenyltransferase-like protein, putative
Trypanosoma brucei Tb927.7.5880   cis-prenyltransferase-like protein
Trypanosoma congolense TcIL3000_7_4880   cis-prenyltransferase-like protein, putative
Trypanosoma cruzi TcCLB.508173.60   cis-prenyltransferase, putative
Toxoplasma gondii TGME49_316770   undecaprenyl diphosphate synthase
Treponema pallidum TP0603   undecaprenyl pyrophosphate synthase
Theileria parva TP03_0421   undecaprenyl diphosphate synthase, putative
Trichomonas vaginalis TVAG_313970   undecaprenyl diphosphate synthase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0804   undecaprenyl pyrophosphate synthase

Essentiality

TP0603 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.7.5880 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.7.5880 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.7.5880 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.7.5880 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b0174 Escherichia coli essential goodall
YBR002C Saccharomyces cerevisiae inviable yeastgenome
TGME49_316770 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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.
  • 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

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
Species Known druggable target Linked compounds Reference
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) Undecaprenyl pyrophosphate 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
0.0026 1 0.5
0.0026 1 0.5
0.018 0.2592 1
0.0026 1 0.5
0.0026 1 0.5
0.0026 1 0.5
0.0026 0.5 0.5

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.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier TP0603 (Treponema pallidum), undecaprenyl pyrophosphate synthase
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