Detailed view for LmjF.34.0890

Basic information

TDR Targets ID: 22072
Leishmania major, DNA-directed RNA polymerase subunit, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 4.1039 | Length (AA): 159 | MW (Da): 17521 | 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

PF01192   RNA polymerase Rpb6

Gene Ontology

Mouse over links to read term descriptions.
GO:0006351   transcription, DNA-dependent  
GO:0005665   DNA-directed RNA polymerase II, core complex  
GO:0030880   RNA polymerase complex  
GO:0005634   nucleus  
GO:0003899   DNA-directed RNA polymerase activity  
GO:0003677   DNA binding  

Metabolic Pathways

Purine metabolism (KEGG)
Pyrimidine metabolism (KEGG)
Global map (KEGG)
RNA polymerase (KEGG)

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
65 148 1twf (F) 72 155 68.00 0 1 1.3 -1.21
1 146 1qkl (A) 801 925 60.00 0 0.98 1.27404 1.34
1 146 1qkl (A) 801 925 55.00 0 1 1.23204 1.42
13 47 5fug (C) 21 65 29.00 0.36 0.01 0.494826 -1
48 147 4c2m (F) 55 154 57.00 0 1 1.34463 -0.52

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_127345)

Species Accession Gene Product
Arabidopsis thaliana AT2G04630   DNA-directed RNA polymerases II and V subunit 6B
Arabidopsis thaliana AT5G51940   RNA polymerase Rpb6
Babesia bovis BBOV_II001260   DNA-directed RNA polymerase subunit I, putative
Brugia malayi Bm1_49350   DNA-directed RNA polymerases I, II, and III 14.4 kDa polypeptide
Candida albicans CaO19.10166   similar to S. cerevisiae RPO26 (YPR187W) subunit common to RNA polymerase I, II and III
Candida albicans CaO19.2643   similar to S. cerevisiae RPO26 (YPR187W) subunit common to RNA polymerase I, II and III
Caenorhabditis elegans CELE_C06A1.5   Protein RPB-6
Cryptosporidium hominis Chro.70529   DNA-directed RNA polymerase IIa
Cryptosporidium parvum cgd7_4770   DNA-directed RNA polymerase subunit
Dictyostelium discoideum DDB_G0291037   RNA polymerase I core subunit
Drosophila melanogaster Dmel_CG1163   RNA polymerase II 18kD subunit
Echinococcus granulosus EgrG_000230200   dna directed rna polymerases i ii and iii
Entamoeba histolytica EHI_088230   DNA-directed RNA polymerases I, II, and III 23 kDa, putative
Echinococcus multilocularis EmuJ_000230200   DNA directed RNA polymerases I, II, and III
Giardia lamblia GL50803_15955   DNA-directed RNA polymerase II RPB6
Homo sapiens ENSG00000100142   polymerase (RNA) II (DNA directed) polypeptide F
Leishmania braziliensis LbrM.20.0860   DNA-directed RNA polymerase subunit, putative
Leishmania donovani LdBPK_340940.1   DNA-directed RNA polymerase subunit, putative
Leishmania infantum LinJ.34.0940   DNA-directed RNA polymerase subunit, putative
Leishmania major LmjF.34.0890   DNA-directed RNA polymerase subunit, putative
Leishmania mexicana LmxM.33.0890   DNA-directed RNA polymerase subunit, putative
Loa Loa (eye worm) LOAG_10547   hypothetical protein
Mus musculus ENSMUSG00000033020   polymerase (RNA) II (DNA directed) polypeptide F
Neospora caninum NCLIV_036000   Polymerase (RNA) II (DNA directed) polypeptide F, related
Oryza sativa 4343168   Os07g0463100
Oryza sativa 4333343   Os03g0586600
Plasmodium berghei PBANKA_0401900   DNA-directed RNA polymerases I, II, and III subunit RPABC2, putative
Plasmodium falciparum PF3D7_0303300   DNA-directed RNA polymerases I, II, and III subunit RPABC2, putative
Plasmodium knowlesi PKNH_0839800   DNA-directed RNA polymerases I, II, and III subunit RPABC2, putative
Plasmodium vivax PVX_119290   DNA-directed RNA polymerases I, II, and III 14.4 kDa polypeptide, putative
Plasmodium yoelii PY01352   Plasmodium vivax PV1H14085_P
Saccharomyces cerevisiae YPR187W   DNA-directed RNA polymerase core subunit RPB6
Schistosoma japonicum Sjp_0071940   ko:K03014 DNA-directed RNA Polymerase II subunit F, putative
Schistosoma mansoni Smp_073570   DNA-directed rna polymerase subunit rpb6
Schmidtea mediterranea mk4.007711.01   DNA-directed RNA polymerases I, II, and III subunit RPABC2
Schmidtea mediterranea mk4.013887.00   DNA-directed RNA polymerases I, II, and III subunit RPABC2
Schmidtea mediterranea mk4.002671.04   DNA-directed RNA polymerases I, II, and III subunit RPABC2
Trypanosoma brucei gambiense Tbg972.4.3500   DNA-directed RNA polymerase subunit, putative
Trypanosoma brucei gambiense Tbg972.4.3515   DNA-directed RNA polymerase subunit, putative
Trypanosoma brucei Tb927.4.3490   DNA-directed RNA polymerases II and III subunit RPB6, putative
Trypanosoma brucei Tb927.4.3510   DNA-directed RNA polymerase subunit, putative
Trypanosoma cruzi TcCLB.506199.5   DNA-directed RNA polymerase subunit, putative
Trypanosoma cruzi TcCLB.507159.90   DNA-directed rna polymerase II subunit, putative
Trypanosoma cruzi TcCLB.507485.15   DNA-directed RNA polymerase subunit, putative
Trypanosoma cruzi TcCLB.507159.44   DNA-directed rna polymerase II subunit, putative
Trypanosoma cruzi TcCLB.507673.65   DNA-directed RNA polymerase subunit, putative
Trypanosoma cruzi TcCLB.507159.65   DNA-directed RNA polymerase subunit, putative
Trypanosoma cruzi TcCLB.507485.34   DNA-directed RNA polymerase III subunit, putative
Toxoplasma gondii TGME49_270780   DNA-directed RNA polymerase II RPB6
Trichomonas vaginalis TVAG_221960   DNA-directed RNA polymerase subunit rpb6, putative
Trichomonas vaginalis TVAG_348020   DNA-directed RNA polymerase subunit rpb6, putative
Trichomonas vaginalis TVAG_352310   DNA-directed RNA polymerase subunit rpb6, putative

Essentiality

LmjF.34.0890 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.3490 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.3490 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.4.3490 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.4.3490 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C06A1.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_C06A1.5 Caenorhabditis elegans slow growth wormbase
CELE_C06A1.5 Caenorhabditis elegans sterile wormbase
YPR187W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0401900 Plasmodium berghei Essential plasmo
TGME49_270780 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

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

  • 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

23 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 LmjF.34.0890 (Leishmania major), DNA-directed RNA polymerase subunit, putative
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