Detailed view for TcCLB.504105.30

Basic information

TDR Targets ID: 40403
Trypanosoma cruzi, DNA-directed RNA polymerase III subunit C1, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.5593 | Length (AA): 1553 | MW (Da): 173229 | Paralog Number: 2

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

PF00623   RNA polymerase Rpb1, domain 2
PF04983   RNA polymerase Rpb1, domain 3
PF04997   RNA polymerase Rpb1, domain 1
PF04998   RNA polymerase Rpb1, domain 5
PF05000   RNA polymerase Rpb1, domain 4

Gene Ontology

Mouse over links to read term descriptions.
GO:0006351   transcription, DNA-dependent  
GO:0003899   DNA-directed RNA polymerase activity  
GO:0003677   DNA binding  
GO:0006350   transcription  

Metabolic Pathways

Purine metabolism (KEGG)
Pyrimidine metabolism (KEGG)
Global map (KEGG)
RNA polymerase (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
13 1525 2a6h (D) 2 1504 19.00 0 1 0.45 1.19
22 1507 1twf (A) 8 1446 35.00 0 1 1.17 0.45
13 370 3qqc (A) 53 426 30.00 0 1 0.366622 0.74
19 1507 5xog (A) 5 1449 34.00 0 1 1.18519 0.96
21 1533 3h0g (A) 9 1488 31.00 0 1 1.08764 1.79
24 928 4ayb (A) 3 872 39.00 0 1 0.882143 1.13
914 1130 4tql (A) 23 231 14.00 0.69 0.15 0.27513 -0.58

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_126637)

Species Accession Gene Product
Arabidopsis thaliana ArthCp013   RNA polymerase beta' chain
Arabidopsis thaliana AT4G35800   DNA-directed RNA polymerase II subunit RPB1
Arabidopsis thaliana AT5G60040   nuclear RNA polymerase C1
Babesia bovis BBOV_I003360   DNA-directed RNA polymerase II largest subunit, putative
Babesia bovis BBOV_V000120   rpoC1
Babesia bovis BBOV_III007400   RNA polymerase Rpb1, domain containing protein
Brugia malayi Bm1_27995   RNA polymerase Rpb1, domain 1 family protein
Brugia malayi Bm1_34315   DNA-directed RNA polymerase II largest subunit, putative
Candida albicans CaO19.10615   RNA polymerase 3 large subunit
Candida albicans CaO19.7655   RNA polymerase II large subunit
Candida albicans CaO19.3103   RNA polymerase 3 large subunit
Caenorhabditis elegans CELE_F36A4.7   Protein AMA-1
Caenorhabditis elegans CELE_C42D4.8   Protein RPC-1
Cryptosporidium hominis Chro.30301   DNA-directed RNA polymerase (EC 2.7.7.6) II largest chain
Cryptosporidium hominis Chro.60382   DNA-directed RNA polymerase II/III subunit
Cryptosporidium parvum cgd6_3290   DNA-directed RNA polymerase III C1 subunit
Cryptosporidium parvum cgd3_2620   putative DNA-directed RNA polymerase,possible RNA polymerase A/beta/A subunit, long PHYSPTS repeat at C-terminus
Chlamydia trachomatis CT_314   DNA-directed RNA polymerase subunit beta'
Dictyostelium discoideum DDB_G0277199   RNA polymerase III, largest subunit
Dictyostelium discoideum DDB_G0279193   RNA polymerase II core subunit
Drosophila melanogaster Dmel_CG17209   CG17209 gene product from transcript CG17209-RC
Drosophila melanogaster Dmel_CG1554   RNA polymerase II 215kD subunit
Escherichia coli b3988   RNA polymerase, beta prime subunit
Echinococcus granulosus EgrG_000811400   DNA directed RNA polymerase II subunit
Echinococcus granulosus EgrG_000428100   DNA directed RNA polymerase III subunit RPC1
Entamoeba histolytica EHI_125350   DNA-directed RNA polymerase III largest subunit, putative
Entamoeba histolytica EHI_121760   DNA-directed RNA polymerase II large subunit, putative
Echinococcus multilocularis EmuJ_000006100   DNA directed RNA polymerase II subunit RPB1
Echinococcus multilocularis EmuJ_000811400   DNA directed RNA polymerase II subunit
Echinococcus multilocularis EmuJ_000428100   DNA directed RNA polymerase III subunit RPC1
Giardia lamblia GL50803_16223   DNA-directed RNA polymerase subunit A
Giardia lamblia GL50803_89347   DNA-directed RNA polymerase II largest subunit RPB1
Homo sapiens ENSG00000181222   polymerase (RNA) II (DNA directed) polypeptide A, 220kDa
Homo sapiens ENSG00000148606   polymerase (RNA) III (DNA directed) polypeptide A, 155kDa
Leishmania braziliensis LbrM.20.0330   DNA-directed RNA polymerase III largest subunit , putative
Leishmania braziliensis LbrM.31.2950   RNA polymerase ii largest subunit
Leishmania donovani LdBPK_340380.1   DNA-directed RNA polymerase III subunit C1, putative
Leishmania donovani LdBPK_312680.1   RNA polymerase ii largest subunit
Leishmania infantum LinJ.31.2680   RNA polymerase ii largest subunit
Leishmania infantum LinJ.34.0380   DNA-directed RNA polymerase III largest subunit , putative
Leishmania major LmjF.31.2610   RNA polymerase ii largest subunit
Leishmania major LmjF.34.0360   DNA-directed RNA polymerase III largest subunit , putative
Leishmania mexicana LmxM.30.2610   RNA polymerase ii largest subunit
Leishmania mexicana LmxM.33.0360   DNA-directed RNA polymerase III largest subunit , putative
Loa Loa (eye worm) LOAG_05313   DNA-directed RNA polymerase II largest subunit
Loa Loa (eye worm) LOAG_03832   RNA polymerase Rpb1
Mycobacterium leprae ML1890c   DNA-DIRECTED RNA POLYMERASE (BETA' CHAIN) RPOC (TRANSCRIPTASE BETA' CHAIN) (RNA POLYMERASE BETA' SUBUNIT).
Mus musculus ENSMUSG00000025280   polymerase (RNA) III (DNA directed) polypeptide A
Mus musculus ENSMUSG00000005198   polymerase (RNA) II (DNA directed) polypeptide A
Mycobacterium tuberculosis Rv0668   DNA-directed RNA polymerase (beta' chain) RpoC (transcriptase beta' chain) (RNA polymerase beta' subunit).
Mycobacterium ulcerans MUL_0747   DNA-directed RNA polymerase subunit beta'
Neospora caninum NCLIV_047440   DNA-directed RNA polymerase II largest subunit, putative
Neospora caninum NCLIV_044520   DNA-directed RNA polymerase III largest subunit, putative
Oryza sativa 4336254   Os04g0492300
Oryza sativa 9267835   Os08g0155700
Oryza sativa 3131433   RNA polymerase beta' chain
Oryza sativa 4337831   Os05g0151000
Oryza sativa 9271945   Os01g0111900
Plasmodium berghei PBANKA_API00160   RNA polymerase beta subunit, putative
Plasmodium berghei PBANKA_1344000   DNA-directed RNA polymerase III subunit RPC1, putative
Plasmodium berghei PBANKA_0807000   DNA-directed RNA polymerase II subunit RPB1, putative
Plasmodium falciparum PF3D7_API04300   RNA polymerase beta subunit, putative
Plasmodium falciparum PF3D7_1329000   DNA-directed RNA polymerase III subunit RPC1, putative
Plasmodium falciparum PF3D7_0318200   DNA-directed RNA polymerase II subunit RPB1
Plasmodium knowlesi PKNH_API05200   RNA polymerase beta subunit, putative
Plasmodium knowlesi PKNH_0823500   DNA-directed RNA polymerase II subunit RPB1, putative
Plasmodium knowlesi PKNH_1271400   DNA-directed RNA polymerase III subunit RPC1, putative
Plasmodium vivax PVX_082395   DNA-directed RNA polymerase III largest subunit, putative
Plasmodium vivax PVX_095320   DNA-directed RNA polymerase II subunit RPB1, putative
Plasmodium yoelii PY04439   DNA-directed RNA polymerase beta' chain
Plasmodium yoelii PY01037   RNA polymerase A/beta'/A'' subunit, putative
Plasmodium yoelii PY03187   RNA polymerase A/beta'/A'' subunit, putative
Saccharomyces cerevisiae YDL140C   DNA-directed RNA polymerase II core subunit RPO21
Saccharomyces cerevisiae YOR116C   DNA-directed RNA polymerase III core subunit RPO31
Schistosoma japonicum Sjp_0073320   DNA-directed RNA polymerase III subunit RPC1, putative
Schistosoma japonicum Sjp_0130240   DNA-directed RNA polymerase III subunit RPC1, putative
Schistosoma japonicum Sjp_0048890   expressed protein
Schistosoma japonicum Sjp_0108190   DNA-directed RNA polymerase III subunit RPC1, putative
Schistosoma japonicum Sjp_0309240   DNA-directed RNA polymerase II subunit RPB1, putative
Schistosoma japonicum Sjp_0131980   DNA-directed RNA polymerase III subunit RPC1, putative
Schistosoma japonicum Sjp_0130250   DNA-directed RNA polymerase III subunit RPC1, putative
Schistosoma japonicum Sjp_0128360   DNA-directed RNA polymerase II subunit RPB1, putative
Schistosoma japonicum Sjp_0086530   ko:K03006 DNA-directed RNA polymerase II subunit A, putative
Schistosoma mansoni Smp_157740   RNA polymerase Rpb1
Schistosoma mansoni Smp_002890   DNA-directed RNA polymerase III largest subunit
Schistosoma mansoni Smp_156670   DNA-directed RNA polymerase II largest subunit
Schmidtea mediterranea mk4.004362.02   DNA-directed RNA polymerase III subunit RPC1
Schmidtea mediterranea mk4.004768.00   DNA-directed RNA polymerase III subunit RPC1
Schmidtea mediterranea mk4.004362.01   DNA-directed RNA polymerase II subunit RPB1
Schmidtea mediterranea mk4.001978.00   DNA-directed RNA polymerase III subunit RPC1
Schmidtea mediterranea mk4.001789.00  
Trypanosoma brucei gambiense Tbg972.4.5210   RNA polymerase IIA largest subunit, putative
Trypanosoma brucei gambiense Tbg972.8.7660  
Trypanosoma brucei gambiense Tbg972.10.3460   DNA-directed RNA polymerase iii largest subunit,RNA polymerase III largest subunit, putative
Trypanosoma brucei Tb927.8.7400   RNA polymerase IIA largest subunit
Trypanosoma brucei Tb927.10.2780   DNA-directed RNA polymerase III subunit C1
Trypanosoma brucei Tb11.v5.0609   DNA-directed RNA polymerase III largest subunit, putative
Trypanosoma brucei Tb927.4.5020   DNA-directed RNA polymerase II subunit RPB1
Trypanosoma brucei Tb11.v5.0608   DNA-directed RNA polymerase III largest subunit, putative
Trypanosoma brucei Tb11.v5.0504   RNA polymerase IIA largest subunit, putative
Trypanosoma congolense TcIL3000_10_2390   DNA-directed RNA polymerase III subunit C1, putative
Trypanosoma congolense TcIL3000_4_4270   RNA polymerase IIA largest subunit, putative
Trypanosoma cruzi TcCLB.510685.30   RNA polymerase IIA largest subunit, putative
Trypanosoma cruzi TcCLB.509011.20   RNA polymerase IIA largest subunit, putative
Trypanosoma cruzi TcCLB.504105.30   DNA-directed RNA polymerase III subunit C1, putative
Toxoplasma gondii TGME49_306290   DNA-directed RNA polymerase III RPC1
Toxoplasma gondii TGME49_326700   DNA-directed RNA polymerase, putative
Toxoplasma gondii TGME49_225260   DNA-directed RNA polymerase II RPB1
Treponema pallidum TP0242   DNA-directed RNA polymerase subunit beta'
Theileria parva TP04_0648   DNA-directed RNA polymerase III largest subunit, putative
Theileria parva TP03_0185   DNA-directed RNA polymerase II largest subunit, putative
Theileria parva TP05_0029   DNA-directed RNA polymerase beta' chain, putative
Trichomonas vaginalis TVAG_172240   DNA-directed RNA polymerase I largest subunit, putative
Trichomonas vaginalis TVAG_247430   DNA-directed RNA polymerase I largest subunit, putative

Essentiality

TcCLB.504105.30 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.2780 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.10.2780 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.2780 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.2780 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Tb927.4.5020 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.5020 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.4.5020 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.4.5020 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Tb927.8.7400 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.8.7400 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.8.7400 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.8.7400 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b3988 Escherichia coli essential goodall
CELE_F36A4.7 Caenorhabditis elegans embryonic arrest wormbase
CELE_F36A4.7 Caenorhabditis elegans embryonic lethal wormbase
CELE_F36A4.7 Caenorhabditis elegans larval arrest wormbase
CELE_F36A4.7 Caenorhabditis elegans slow growth wormbase
CELE_F36A4.7 Caenorhabditis elegans sterile wormbase
CELE_C42D4.8 Caenorhabditis elegans embryonic lethal wormbase
CELE_C42D4.8 Caenorhabditis elegans larval arrest wormbase
CELE_C42D4.8 Caenorhabditis elegans larval lethal wormbase
CELE_C42D4.8 Caenorhabditis elegans slow growth wormbase
CELE_C42D4.8 Caenorhabditis elegans sterile wormbase
YDL140C Saccharomyces cerevisiae inviable yeastgenome
YOR116C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0807000 Plasmodium berghei Essential plasmo
PBANKA_1344000 Plasmodium berghei Essential plasmo
TGME49_225260 Toxoplasma gondii Probably essential sidik
TGME49_306290 Toxoplasma gondii Probably essential sidik
TGME49_326700 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.
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • 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
  • 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

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

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.00638249 0.278233 0
0.0009 0.2808 0
0.0039 0.3627 0.3768
0.0046 0.3767 0.4194

Assayability

Assay information

  • Assay for Ribonucleic Acid Polymerase (2.7.7.6 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

No reagent availability information for this target.

Bibliographic References

46 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 TcCLB.504105.30 (Trypanosoma cruzi), DNA-directed RNA polymerase III subunit C1, putative
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