Detailed view for LmjF.30.2410

Basic information

TDR Targets ID: 22937
Leishmania major, pre-mRNA cleavage complex II Clp1-like protein
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.7836 | Length (AA): 425 | MW (Da): 45887 | 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

PF16575   mRNA cleavage and polyadenylation factor CLP1 P-loop

Gene Ontology

Mouse over links to read term descriptions.
No GO information for this protein.

Metabolic Pathways

mRNA surveillance pathway (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
28 298 1ls1 (A) 5 249 17.00 0 0.77 0.75 -0.27
126 309 1cp2 (A) 4 189 9.00 0.000037 0.04 0.5 -0.5
9 415 4ohx (A) 7 423 24.00 0 1 1.21895 0.05
32 414 4ohx (A) 31 422 29.00 0 1 1.13388 0.55

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_127602)

Species Accession Gene Product
Arabidopsis thaliana AT5G39930   CLP1-like protein 5
Arabidopsis thaliana AT3G04680   CLP-like protein 3
Babesia bovis BBOV_IV008810   pre-mRNA cleavage complex II protein Clp1, putative
Brugia malayi Bm1_20975   Pre-mRNA cleavage complex II protein Clp1
Candida albicans CaO19.6931   cleavage and polyadenylation factor CF I component
Candida albicans CaO19.14193   cleavage and polyadenylation factor CF I component
Caenorhabditis elegans CELE_F59A2.4   Protein CLPF-1, isoform B
Cryptosporidium hominis Chro.50085   pre-mRNA cleavage complex ii protein clp1-related
Cryptosporidium parvum cgd5_2880   C1p1p GTpase. Pre-mRNA cleavaage complex protein
Dictyostelium discoideum DDB_G0285507   pre-mRNA cleavage complex subunit
Drosophila melanogaster Dmel_CG5970   crowded by cid
Echinococcus granulosus EgrG_000118700   polyribonucleotide 5' hydroxyl kinase Clp1
Entamoeba histolytica EHI_008100   ATP/GTP-binding protein, putative
Echinococcus multilocularis EmuJ_000118700   polyribonucleotide 5' hydroxyl kinase Clp1
Homo sapiens ENSG00000172409   cleavage and polyadenylation factor I subunit 1
Leishmania braziliensis LbrM.30.2360   pre-mRNA cleavage complex II Clp1-like protein
Leishmania donovani LdBPK_302420.1   pre-mRNA cleavage complex II Clp1-like protein
Leishmania infantum LinJ.30.2420   pre-mRNA cleavage complex II Clp1-like protein
Leishmania major LmjF.30.2410   pre-mRNA cleavage complex II Clp1-like protein
Leishmania mexicana LmxM.29.2410   pre-mRNA cleavage complex II Clp1-like protein
Loa Loa (eye worm) LOAG_11732   hypothetical protein
Loa Loa (eye worm) LOAG_06833   hypothetical protein
Mus musculus ENSMUSG00000027079   CLP1, cleavage and polyadenylation factor I subunit
Neospora caninum NCLIV_001590   hypothetical protein
Oryza sativa 4328733   Os02g0217500
Plasmodium berghei PBANKA_0709200   polyribonucleotide 5'-hydroxyl-kinase Clp1, putative
Plasmodium falciparum PF3D7_0821600   polyribonucleotide 5'-hydroxyl-kinase Clp1, putative
Plasmodium knowlesi PKNH_1315600   polyribonucleotide 5'-hydroxyl-kinase Clp1, putative
Plasmodium vivax PVX_089285   hypothetical protein, conserved
Plasmodium yoelii PY04248   pre-mRNA cleavage complex ii protein clp1-related
Saccharomyces cerevisiae YOR250C   Clp1p
Schistosoma japonicum Sjp_0062400   Pre-mRNA cleavage complex II protein Clp1, putative
Schistosoma mansoni Smp_019130   cleavage/polyadenylation factor ia subunit clp1p
Schmidtea mediterranea mk4.017186.00   Protein CLP1 homolog
Schmidtea mediterranea mk4.001470.04  
Schmidtea mediterranea mk4.004365.02   Protein CLP1 homolog
Trypanosoma brucei gambiense Tbg972.6.3460   pre-mRNA cleavage complex II Clp1-like, conserved, putative
Trypanosoma brucei Tb927.6.3690   pre-mRNA cleavage complex II Clp1-like, conserved
Trypanosoma congolense TcIL3000_6_3250   pre-mRNA cleavage complex II Clp1-like, conserved, putative
Trypanosoma congolense TcIL3000_0_32350   pre-mRNA cleavage complex II Clp1-like, conserved
Trypanosoma cruzi TcCLB.507027.59   pre-mRNA cleavage complex II Clp1 protein, putative
Trypanosoma cruzi TcCLB.506941.229   pre-mRNA cleavage complex II Clp1 protein, putative
Theileria parva TP01_0895   hypothetical protein
Trichomonas vaginalis TVAG_162880   pre-mRNA cleavage complex II protein Clp1, putative
Trichomonas vaginalis TVAG_317830   conserved hypothetical protein

Essentiality

LmjF.30.2410 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.6.3690 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.6.3690 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.6.3690 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.6.3690 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F59A2.4 Caenorhabditis elegans embryonic lethal wormbase
CELE_F59A2.4 Caenorhabditis elegans larval arrest wormbase
CELE_F59A2.4 Caenorhabditis elegans sterile wormbase
YOR250C Saccharomyces cerevisiae inviable yeastgenome
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • 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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Gene identifier LmjF.30.2410 (Leishmania major), pre-mRNA cleavage complex II Clp1-like protein
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