Detailed view for LmjF.35.1700

Basic information

TDR Targets ID: 25052
Leishmania major, RNA 3-terminal phosphate cyclase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.9452 | Length (AA): 362 | MW (Da): 39175 | 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

PF01137   RNA 3'-terminal phosphate cyclase
PF05189   RNA 3'-terminal phosphate cyclase (RTC), insert domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005730   nucleolus  
GO:0003824   catalytic activity  
GO:0042254   ribosome biogenesis and assembly  
GO:0006396   RNA processing  

Metabolic Pathways

Ribosome biogenesis in eukaryotes (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
1 334 1qmh (A) 5 331 19.00 0 1 1.15 -1.11
1 352 3pqv (A) 7 354 29.00 0 1 1.37428 -0.69
3 356 4clq (A) 10 361 27.00 0 1 1.4018 -0.85

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
Lower 20-40% 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_127812)

Species Accession Gene Product
Arabidopsis thaliana AT5G22100   RNA 3'-terminal phosphate cyclase-like protein
Babesia bovis BBOV_IV007230   RNA 3'-terminal phosphate cyclase, putative
Brugia malayi Bm1_10025   Probable RNA 3'-terminal phosphate cyclase-like protein
Candida albicans CaO19.9442   RNA 3'-terminal phosphate cyclase similar to S. cerevisiae RCL1 involved in rRNA processing
Candida albicans CaO19.1886   RNA 3'-terminal phosphate cyclase similar to S. cerevisiae RCL1 involved in rRNA processing
Caenorhabditis elegans CELE_ZK1127.5   Protein ZK1127.5
Cryptosporidium hominis Chro.80423   RNA 3-Terminal Phosphate Cyclase-like protein
Cryptosporidium parvum cgd8_3660   RNA 3-Terminal Phosphate Cyclase-like protein
Dictyostelium discoideum DDB_G0282803   RNA 3'-terminal phosphate cyclase family protein
Drosophila melanogaster Dmel_CG11130   CG11130 gene product from transcript CG11130-RA
Echinococcus granulosus EgrG_000646400   RNA 3' terminal phosphate cyclase protein
Entamoeba histolytica EHI_115370   RNA 3-terminal phosphate cyclase, putative
Echinococcus multilocularis EmuJ_000646400   RNA 3' terminal phosphate cyclase protein
Giardia lamblia GL50803_6590   RNA 3-terminal phosphate cyclase-like protein
Homo sapiens ENSG00000120158   RNA terminal phosphate cyclase-like 1
Leishmania braziliensis LbrM.34.1610   RNA 3-terminal phosphate cyclase, putative
Leishmania donovani LdBPK_351700.1   RNA re-capping enzyme, cytoplasmic, putative
Leishmania infantum LinJ.35.1700   RNA 3-terminal phosphate cyclase, putative
Leishmania major LmjF.35.1700   RNA 3-terminal phosphate cyclase, putative
Leishmania mexicana LmxM.34.1700   RNA 3-terminal phosphate cyclase, putative
Loa Loa (eye worm) LOAG_02169   hypothetical protein
Mus musculus ENSMUSG00000024785   RNA terminal phosphate cyclase-like 1
Neospora caninum NCLIV_032370   rna 3 terminal phosphate cyclase, putative
Oryza sativa 4334688   Os03g0833700
Plasmodium berghei PBANKA_1334200   RNA 3'-terminal phosphate cyclase-like protein, putative
Plasmodium falciparum PF3D7_1471000   RNA 3'-terminal phosphate cyclase-like protein, putative
Plasmodium knowlesi PKNH_1210000   RNA 3'-terminal phosphate cyclase-like protein, putative
Plasmodium vivax PVX_116920   RNA 3'-terminal phosphate cyclase-like protein, putative
Plasmodium yoelii PY05891   probable RNA 3'-terminal phosphate cyclase-like protein
Saccharomyces cerevisiae YOL010W   Rcl1p
Schistosoma japonicum Sjp_0015290   ko:K01974 RNA-3'-phosphate cyclase [EC6.5.1.4], putative
Schistosoma mansoni Smp_102450   rna 3' terminal phosphate cyclase
Schmidtea mediterranea mk4.000449.00   Putative rna 3' terminal phosphate cyclase
Trypanosoma brucei gambiense Tbg972.9.9050   RNA 3-terminal phosphate cyclase-like protein, putative
Trypanosoma brucei Tb927.9.14410   RNA re-capping enzyme, cytoplasmic
Trypanosoma congolense TcIL3000_9_6200   RNA re-capping enzyme, cytoplasmic, putative
Trypanosoma cruzi TcCLB.510761.30   RNA re-capping enzyme, cytoplasmic, putative
Toxoplasma gondii TGME49_232390   18S rRNA biogenesis protein RCL1 protein
Theileria parva TP03_0231   RNA 3'-terminal phosphate cyclase, putative

Essentiality

LmjF.35.1700 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.4870 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.211.4870 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.211.4870 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.211.4870 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_ZK1127.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_ZK1127.5 Caenorhabditis elegans larval arrest wormbase
CELE_ZK1127.5 Caenorhabditis elegans larval lethal wormbase
CELE_ZK1127.5 Caenorhabditis elegans slow growth wormbase
CELE_ZK1127.5 Caenorhabditis elegans sterile wormbase
YOL010W Saccharomyces cerevisiae inviable yeastgenome
TGME49_232390 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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.
  • 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
  • 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
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource

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.

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User comments

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Gene identifier LmjF.35.1700 (Leishmania major), RNA 3-terminal phosphate cyclase, putative
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