Detailed view for LmjF.01.0220

Basic information

TDR Targets ID: 25257
Leishmania major, cyclophilin 12, putative

Source Database / ID:  TriTrypDB  GeneDB

pI: 5.8966 | Length (AA): 335 | MW (Da): 36187 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG2

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

PF00160   Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD

Gene Ontology

Mouse over links to read term descriptions.
GO:0000413   protein peptidyl-prolyl isomerization  
GO:0003755   peptidyl-prolyl cis-trans isomerase activity  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 8 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
136 333 1ihg (A) 2 186 35.00 0 1 1.06 -1.04
149 331 2gw2 (A) 7 177 39.00 0 1 1.09 -1.33
163 308 1xyh (A) 9 131 38.00 0 0.9 0.73 -0.37
137 333 1ihg (A) 3 186 30.00 0.0000000089 1 0.97016 -0.65
144 331 1a58 (A) 1 176 39.00 0 1 1.04299 -0.63
144 331 3k2c (A) 1 169 44.00 0 1 1.02299 -0.63
150 331 2he9 (A) 7 176 37.00 0.00000001 1 1.01138 -0.81
169 334 2b71 (A) 53 190 44.00 0 0.99 0.793322 0.2

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
Mid 40-60% 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_133785)

Species Accession Gene Product
Echinococcus granulosus EgrG_000477000   peptidyl prolyl cis trans isomerase 6
Echinococcus multilocularis EmuJ_000477000   peptidyl prolyl cis trans isomerase 6
Homo sapiens ENSG00000185250   peptidylprolyl isomerase (cyclophilin)-like 6
Leishmania braziliensis LbrM.01.0250   cyclophilin 12, putative
Leishmania donovani LdBPK_010220.1   cyclophilin type peptidyl-prolyl cis-trans isomerase, putative
Leishmania infantum LinJ.01.0220   cyclophilin 12, putative
Leishmania major LmjF.01.0220   cyclophilin 12, putative
Leishmania mexicana LmxM.01.0220   cyclophilin type peptidyl-prolyl cis-trans isomerase, putative
Mus musculus ENSMUSG00000078451   peptidylprolyl isomerase (cyclophilin)-like 6
Schistosoma japonicum Sjp_0070260   ko:K01802 peptidylprolyl isomerase [EC5.2.1.8], putative
Schistosoma mansoni Smp_054330   cyclophilin
Schmidtea mediterranea mk4.000351.04   Peptidyl-prolyl cis-trans isomerase-like 6
Trypanosoma brucei gambiense Tbg972.9.1740   cyclophilin type peptidyl-prolyl cis-trans isomerase, putative
Trypanosoma brucei Tb927.9.3440   cyclophilin type peptidyl-prolyl cis-trans isomerase, putative
Trypanosoma congolense TcIL3000_9_1010   cyclophilin type peptidyl-prolyl cis-trans isomerase, putative
Trypanosoma cruzi TcCLB.504797.100   rotamase, putative
Trypanosoma cruzi TcCLB.511577.40   35 kDa cyclophilin, putative
Toxoplasma gondii TGME49_204325   hypothetical protein

Essentiality

LmjF.01.0220 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.160.2070 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb09.160.2070 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.160.2070 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb09.160.2070 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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.
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
Species Target Length Identity Alignment span Linked Drugs Reference
Rattus norvegicus Cyclophilin A 164 aa 36.9% 179 aa Compounds References
Plasmodium falciparum peptidyl-prolyl cis-trans isomerase 171 aa 38.8% 183 aa Compounds References

Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

  • Assay for FK-Binding Protein Peptidyl-Prolyl Isomerase Activity (5.2.1.8 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

  • Lmaj00307AAA;
  • Type Source Notes
    soluble recombinant protein Structural Genomics for Pathogenic Protozoa (SGPP) Lmaj00307; Recombinant protein: full-length; Source: L major; cyclophilin type peptidyl-prolyl cis-trans isomerase putative; old ID AAC24632 ;

Bibliographic References

5 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.

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Gene identifier LmjF.01.0220 (Leishmania major), cyclophilin 12, putative
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