Detailed view for TcCLB.506685.30

Basic information

TDR Targets ID: 43821
Trypanosoma cruzi, thymidylate kinase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.8182 | Length (AA): 351 | MW (Da): 39338 | Paralog Number: 1

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

Druggability Group : DG4

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

PF02223   Thymidylate kinase

Gene Ontology

Mouse over links to read term descriptions.
GO:0005524   ATP binding  
GO:0004798   thymidylate kinase activity  
GO:0006233   dTDP biosynthetic process  

Metabolic Pathways

Pyrimidine metabolism (KEGG)
Global map (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
131 308 3tmk (A) 6 165 28.00 0.00000026 0.85 0.775622 -0.18
132 347 1nn5 (A) 8 199 31.00 0 1 0.933785 -0.85
132 308 1nn5 (A) 8 173 34.00 0.0000000000064 1 0.794774 -0.15

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 epimastigote. Smircich P
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile metacyclic. Smircich P
Show/Hide expression data references
  • Smircich P Ribosome profiling reveals translation control as a key mechanism generating differential gene expression in Trypanosoma cruzi.

Orthologs

Ortholog group members (OG5_126920)

Species Accession Gene Product
Arabidopsis thaliana AT5G59440   protein ZEU1 (ZEUS1)
Babesia bovis BBOV_III006440   thymidylate kinase, putative
Brugia malayi Bm1_23075   thymidylate kinase
Candida albicans CaO19.1137   Thymidylate kinase
Candida albicans CaO19.8730   Thymidylate kinase
Caenorhabditis elegans CELE_R53.2   Protein R53.2
Cryptosporidium hominis Chro.50490   thymidylate kinase
Cryptosporidium parvum cgd5_3630   thymidylate kinase
Chlamydia trachomatis CT_188   thymidylate kinase
Dictyostelium discoideum DDB_G0290033   dTMP kinase
Drosophila melanogaster Dmel_CG5757   CG5757 gene product from transcript CG5757-RB
Escherichia coli b1098   thymidylate kinase
Echinococcus granulosus EgrG_000756200   thymidylate kinase
Entamoeba histolytica EHI_008040   Thymidylate kinase, putative
Echinococcus multilocularis EmuJ_000756200   thymidylate kinase
Giardia lamblia GL50803_15380   CDC8
Homo sapiens ENSG00000168393   deoxythymidylate kinase (thymidylate kinase)
Leishmania braziliensis LbrM.10.0060   thymidylate kinase-like protein
Leishmania donovani LdBPK_100040.1   thymidylate kinase-like protein
Leishmania infantum LinJ.10.0040   thymidylate kinase-like protein
Leishmania major LmjF.10.0060   thymidylate kinase-like protein
Leishmania mexicana LmxM.10.0060   thymidylate kinase-like protein
Loa Loa (eye worm) LOAG_01297   thymidylate kinase
Mycobacterium leprae ML0772   probable thymidylate kinase Tmk (dTMP KINASE) (THYMIDYLIC ACID KINASE) (TMPK)
Mus musculus ENSMUSG00000026281   deoxythymidylate kinase
Mycobacterium tuberculosis Rv3247c   Thymidylate kinase Tmk (dTMP kinase) (thymidylic acid kinase) (TMPK)
Mycobacterium ulcerans MUL_2583   thymidylate kinase
Neospora caninum NCLIV_053180   Thymidylate kinase, related
Oryza sativa 4344056   Os07g0639900
Onchocerca volvulus OVOC10889   Putative thymidylate kinase
Plasmodium berghei PBANKA_1464200   thymidylate kinase, putative
Plasmodium falciparum PF3D7_1251300   thymidylate kinase
Plasmodium knowlesi PKNH_1471300   thymidylate kinase, putative
Plasmodium vivax PVX_101455   thymidylate kinase, putative
Plasmodium yoelii PY01336   Thymidylate kinase
Saccharomyces cerevisiae YJR057W   bifunctional thymidylate/uridylate kinase
Schistosoma japonicum Sjp_0008250   ko:K00943 dTMP kinase [EC2.7.4.9], putative
Schistosoma japonicum Sjp_0056420   Thymidylate kinase, putative
Schistosoma mansoni Smp_027740   hypothetical protein
Schistosoma mansoni Smp_032810   thymidylate kinase
Schistosoma mansoni Smp_001360   thymidylate kinase
Schmidtea mediterranea mk4.014274.01  
Schmidtea mediterranea mk4.004278.02  
Schmidtea mediterranea mk4.001266.05   Probable thymidylate kinase
Trypanosoma brucei gambiense Tbg972.8.3620   thymidylate kinase, putative
Trypanosoma brucei Tb11.v5.0738   thymidylate kinase, putative
Trypanosoma brucei Tb927.8.3510   thymidylate kinase, putative
Trypanosoma congolense TcIL3000_0_00560   thymidylate kinase, putative
Trypanosoma congolense TcIL3000_8_3770   thymidylate kinase, putative
Trypanosoma cruzi TcCLB.506685.30   thymidylate kinase, putative
Trypanosoma cruzi TcCLB.509663.30   thymidylate kinase, putative
Toxoplasma gondii TGME49_306970   thymidylate kinase
Treponema pallidum TP0354   thymidylate kinase (tmk)
Theileria parva TP02_0319   thymidylate kinase, putative
Trichomonas vaginalis TVAG_134830   thymidylate kinase, putative
Trichomonas vaginalis TVAG_315260   thymidylate kinase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0148   thymidylate kinase

Essentiality

TcCLB.506685.30 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.3910 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.8.3910 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.8.3910 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.8.3910 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Tb927.8.3510 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.8.3510 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.8.3510 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.8.3510 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b1098 Escherichia coli essential goodall
CELE_R53.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_R53.2 Caenorhabditis elegans larval arrest wormbase
YJR057W Saccharomyces cerevisiae inviable yeastgenome
TGME49_306970 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • 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

Druggability index (range: 0 to 1): 0.6

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
Plasmodium falciparum thymidylate kinase Compounds References
Homo sapiens deoxythymidylate kinase (thymidylate kinase) Compounds References
Mycobacterium tuberculosis Thymidylate kinase Tmk (dTMP kinase) (thymidylic acid kinase) (TMPK) 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
0.0516 0.323 1
0.0292 1 1
0.0074 0.5 0.5
0.1122 0.3644 1
0.0365 0.3803 0.6755
0.0293 0.9097 1
0.1122 0.3644 1
0.0087 0.4113 1
0.0367 1 1
0.057 1 1
0.007 0.5 0.5
0.0369 1 1
0.0073 0.3529 1
0.0141 0.3343 0.4615
0.0344 0.7508 1
0.007 0.7315 1
0.0446 0.5 0.5
0.0323 0.3946 1
0.0154 0.2711 0.2646
0.0302 0.331 1
0.0311 0.26 1
0.0087 0.8037 0.8037
0.0365 0.3803 0.6755
0.016 0.2944 0.7956
0.1122 0.3644 1
0.0362 0.7093 1
0.053 1 1
0.0087 0.5135 0.5135
0.0073 1 1
0.1122 0.3644 1
0.0215 1 1
0.036 1 1
0.1122 0.3644 1
0.0142 0.266 0.266
0.0285 0.2693 0.2671
0.0291 1 0.5
0.0306 0.7167 1
0.053 1 1
0.0824 1 1
0.0084 0.2522 0.2185
0.00658401 1 0.5
0.00844282 1 1
0.0212 0.817 1
0.0447 1 1
0.0228 1 1
0.0154 0.2711 0.2646
0.0122 0.4015 0.5
0.0154 0.2711 0.2646
0.0154 0.3913 1
0.0087 0.8037 0.8037
0.0285 0.2693 0.2671
0.0285 0.5149 1
0.0145 0.4141 0.5523
0.0457 0.5658 1
0.0373 1 1
0.0087 0.2715 1
0.0227 0.3572 1
0.0229 1 1
0.00844282 1 1
0.0072 0.2566 1
0.0367 1 1
0.014 0.2676 0.254
0.051 0.4201 1
0.0371 1 1
0.0525 1 1
0.0144 0.2623 0.2598
0.0073 0.3529 1
0.0155 1 1
0.0302 0.331 1
0.0283 0.2693 0.2689
0.0087 0.5 0.5
0.0212 0.817 1
0.0219 0.3664 0.312
0.0365 0.3803 0.6755
0.0449 0.3248 1
0.09 1 1
0.0195606 0.448021 1
0.0445 0.2976 1
0.0087 1 1
0.0154 0.2711 0.2646
0.0687 1 1
0.0155 0.2985 0.2985
0.0073 0.2864 0.2864
0.0538 0.5 0.5
0.014 0.2676 0.254
0.0122 0.4015 0.5
0.0141 0.4992 1
0.0154 0.3913 1
0.0125 0.5307 1
0.0297203 1 1
0.0285 0.5149 1
0.0673 1 1
0.0081 0.4113 1
0.0824 1 1
0.0372 1 1
0.0207691 1 1
0.0229 1 1
0.0087 0.8037 0.8037
0.0367 1 1
0.0691 1 1
0.0122 0.3964 1
0.0358 0.5 0.5
0.0292 1 1
0.0071 0.5 0.5
0.0073 0.3529 1
0.0306 0.7167 1
0.0365 0.3803 0.6755
0.0447 1 1
0.0691 1 1
0.0221 0.5 0.5
0.0161 0.5 0.5
0.0693 0.5 0.5
0.0282 1 1
0.057 1 1
0.0422 0.2541 1
0.0296 0.6225 1
0.0207691 1 1
0.037 0.5 0.5
0.0687 0.6229 0.5
0.0365 0.3803 0.6755
0.051 0.4201 1
0.0829 1 1
0.0125 1 1
0.0087 1 1
0.0087 0.4267 0.74
0.0374 0.3475 1
0.0298 0.2743 0.2732
0.0145 1 1
0.0219 0.3406 1
0.0221 0.6512 1
0.0087 1 1
0.0302 1 1
0.0154 0.3913 1
0.0072 0.3984 1
0.0296 0.6225 1
0.0291 0.2651 0.5284
0.0293 0.9097 1
0.0253 0.3376 0.5
0.0291 1 0.5
0.0071 0.3392 0.5
0.0668 0.7591 1
0.0516 0.323 1
0.0683 0.5 0.5
0.0445 0.2976 1
0.0125 1 1
0.0355 0.5 0.5
0.0227 0.3572 1
0.0142 0.2501 0.2501
0.0073 0.2714 0.2714
0.0106404 0.895283 0.895283
0.0219 0.3664 0.312
0.0294 1 1
0.0292 1 1
0.0212 0.817 1

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 TcCLB.506685.30 (Trypanosoma cruzi), thymidylate kinase, putative
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