Detailed view for Rv1540

Basic information

TDR Targets ID: 981150
Mycobacterium tuberculosis, Conserved hypothetical protein member of yabO/yceC/yfiI family
Source Database / ID:  Tuberculist 

pI: 8.5052 | Length (AA): 308 | MW (Da): 33017 | Paralog Number: 1

Signal peptide: N | GPI Anchor: | 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

PF00849  
PF01479  

Gene Ontology

Mouse over links to read term descriptions.
GO:0009982   pseudouridine synthase activity  
GO:0003723   RNA binding  
GO:0009451   RNA modification  
GO:0001522   pseudouridine synthesis  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 4 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 42 1ogd (A) 26 65 48.00 0.28 0.3 0.447364 1.37
5 307 2ist (A) 8 315 33.00 0 1 1.29717 0.33
16 77 5z81 (A) 11 73 27.00 0.00017 0.71 0.587799 -0.63
82 305 1v9k (A) 94 316 33.00 0 1 1.08467 -0.1

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_126865)

Species Accession Gene Product
Arabidopsis thaliana AT1G76050   RNA pseudourine synthase 2
Arabidopsis thaliana AT5G51140   RNA pseudourine synthase 7
Babesia bovis BBOV_III011610   RNA pseudouridylate synthase family protein
Brugia malayi Bm1_14425   Hypothetical 50.0 kDa protein K07E8.7 in chromosome IV, putative
Candida albicans CaO19.3177   DRAP deaminase
Candida albicans CaO19.10687   DRAP deaminase
Caenorhabditis elegans CELE_K07E8.7   Protein K07E8.7
Cryptosporidium hominis Chro.20259   N-terminal part related to RNA:pseudouridine (psi)-synthases C-terminal portion contains the deaminase domain implicated in Ribo
Cryptosporidium parvum cgd2_2420   Yd1036cp-like RluD, S4+type 1 pseudouridine synthase
Chlamydia trachomatis CT_658   pseudouridine synthase
Dictyostelium discoideum DDB_G0281097   pseudouridine synthase family protein
Dictyostelium discoideum DDB_G0280463   hypothetical protein
Drosophila melanogaster Dmel_CG6187   CG6187 gene product from transcript CG6187-RA
Drosophila melanogaster Dmel_CG31719   CG31719 gene product from transcript CG31719-RD
Escherichia coli b2594   23S rRNA pseudouridine(1911,1915,1917) synthase
Escherichia coli b1086   23S rRNA pseudouridine(955,2504,2580) synthase
Echinococcus granulosus EgrG_001171400   ribosomal pseudouridine synthase
Entamoeba histolytica EHI_037220   hypothetical protein, conserved
Entamoeba histolytica EHI_124370   RNA pseudouridylate synthase, putative
Echinococcus multilocularis EmuJ_001171400   ribosomal pseudouridine synthase
Giardia lamblia GL50803_16328   DRAP deaminase
Homo sapiens ENSG00000166133   RNA pseudouridylate synthase domain containing 2
Leishmania braziliensis LbrM.34.5050   hypothetical protein, conserved
Leishmania infantum LinJ.35.5430   hypothetical protein, conserved
Leishmania major LmjF.35.5110   hypothetical protein, conserved
Leishmania mexicana LmxM.34.5110   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_08790   hypothetical protein
Mycobacterium leprae ML1200   possible pseudouridine synthase
Mus musculus 271842   RNA pseudouridylate synthase domain containing 2
Mycobacterium tuberculosis Rv1540   Conserved hypothetical protein member of yabO/yceC/yfiI family
Mycobacterium tuberculosis Rv3300c   Conserved hypothetical protein
Mycobacterium ulcerans MUL_1538   RluA family pseudouridine synthase
Mycobacterium ulcerans MUL_2659   pseudouridine synthase
Neospora caninum NCLIV_059120   RNA pseudouridylate synthase domain-containing protein, putative
Neospora caninum NCLIV_009500   hypothetical protein
Neospora caninum NCLIV_020280   YDL036Cp-like protein, related
Oryza sativa 4342081   Os06g0717400
Onchocerca volvulus OVOC11280  
Plasmodium berghei PBANKA_0815000   pseudouridylate synthase, putative
Plasmodium falciparum PF3D7_0914000   pseudouridylate synthase, putative
Plasmodium knowlesi PKNH_0711900   pseudouridylate synthase, putative
Plasmodium vivax PVX_099125   pseudouridylate synthase, putative
Plasmodium yoelii PY02484   RNA pseudouridylate synthase, putative
Saccharomyces cerevisiae YDL036C   pseudouridine synthase PUS9
Saccharomyces cerevisiae YOL066C   bifunctional DRAP deaminase/tRNA pseudouridine synthase RIB2
Schistosoma japonicum Sjp_0097370   expressed protein
Schistosoma japonicum Sjp_0203660   ko:K01718 pseudouridylate synthase [EC4.2.1.70], putative
Schistosoma mansoni Smp_106370   ribosomal pseudouridine synthase
Schistosoma mansoni Smp_047860   ribosomal pseudouridine synthase
Schmidtea mediterranea mk4.000536.07  
Trypanosoma brucei gambiense Tbg972.3.2080   hypothetical protein, conserved
Trypanosoma brucei Tb927.3.2130   RNA pseudouridylate synthase, putative
Trypanosoma congolense TcIL3000_3_1240   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.507081.70   hypothetical protein, conserved
Toxoplasma gondii TGME49_205410   RNA pseudouridine synthase superfamily protein
Toxoplasma gondii TGME49_316680   RNA pseudouridine synthase superfamily protein
Treponema pallidum TP0339   hypothetical protein
Theileria parva TP01_1009   hypothetical protein, conserved
Trichomonas vaginalis TVAG_451040   ribosomal pseudouridine synthase, putative

Essentiality

Rv1540 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.3.2130 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.3.2130 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.3.2130 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.3.2130 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b1086 Escherichia coli non-essential goodall
b2594 Escherichia coli essential goodall
YOL066C Saccharomyces cerevisiae inviable yeastgenome
TGME49_316680 Toxoplasma gondii Probably non-essential sidik
TGME49_205410 Toxoplasma gondii Probably non-essential sidik
TGME49_316680 Toxoplasma gondii Probably essential sidik
TGME49_205410 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.
  • 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.
  • 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
  • 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
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

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

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.

User comments

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Gene identifier Rv1540 (Mycobacterium tuberculosis), Conserved hypothetical protein member of yabO/yceC/yfiI family
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