Detailed view for LmjF.07.0060

Basic information

TDR Targets ID: 23086
Leishmania major, cytochrome c1, heme protein, mitochondrial precursor, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.4377 | Length (AA): 258 | MW (Da): 29878 | 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

PF02167   Cytochrome C1 family

Gene Ontology

Mouse over links to read term descriptions.
GO:0020037   heme binding  
GO:0009055   electron carrier activity  
GO:0005506   iron ion binding  

Metabolic Pathways

Oxidative phosphorylation (KEGG)
Global map (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
2 257 2a06 (D) 1 241 42.00 0 1 1.37 0.05
9 257 1ezv (D) 70 306 45.00 0 1 1.46 -0.04
2 257 2a06 (D) 1 241 42.00 0 1 1.41985 0.14
2 257 3cx5 (D) 65 306 45.00 0 1 1.46585 0.08

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_128006)

Species Accession Gene Product
Arabidopsis thaliana AT5G40810   cytochrome c1
Arabidopsis thaliana AT3G27240   ubiquinol-cytochrome c reductase cytochrome c1 subunit
Babesia bovis BBOV_II002550   cytochrome C1 precursor protein, putative
Brugia malayi Bm1_26800   Cytochrome C1 family protein
Candida albicans CaO19.3527   likely cytochrome C1 similar to S. cerevisiae CYT1 (YOR065W) mitochondrial electron transporter
Caenorhabditis elegans CELE_C54G4.8   Protein CYC-1
Dictyostelium discoideum DDB_G0292594   cytochrome c1
Drosophila melanogaster Dmel_CG14508   CG14508 gene product from transcript CG14508-RA
Drosophila melanogaster Dmel_CG4769   CG4769 gene product from transcript CG4769-RA
Echinococcus granulosus EgrG_000190600   ubiquinol cytochrome c reductase cytochrome c1
Echinococcus multilocularis EmuJ_000190600   ubiquinol cytochrome c reductase cytochrome c1
Homo sapiens ENSG00000179091   cytochrome c-1
Leishmania braziliensis LbrM.07.0060   cytochrome c1, heme protein, mitochondrial precursor, putative
Leishmania donovani LdBPK_070210.1   cytochrome c1, heme protein, mitochondrial, putative
Leishmania infantum LinJ.07.0210   cytochrome c1, heme protein, mitochondrial precursor, putative
Leishmania major LmjF.07.0060   cytochrome c1, heme protein, mitochondrial precursor, putative
Leishmania mexicana LmxM.07.0060   cytochrome c1, heme protein, mitochondrial precursor, putative
Loa Loa (eye worm) LOAG_04183   cytochrome C1 family protein
Mus musculus ENSMUSG00000022551   cytochrome c-1
Neospora caninum NCLIV_063330   Ubiquinol-cytochrome c reductase cytochrome c1 subunit (EC 1.10.2.2), related
Oryza sativa 4326795   Os01g0935700
Oryza sativa 4338350   Os05g0301700
Plasmodium berghei PBANKA_1326300   cytochrome c1 precursor, putative
Plasmodium falciparum PF3D7_1462700   cytochrome c1 precursor, putative
Plasmodium knowlesi PKNH_1218800   cytochrome c1 precursor, putative
Plasmodium vivax PVX_117325   cytochrome c1 precursor, putative
Plasmodium yoelii PY03278   cytochrome c1, heme protein
Saccharomyces cerevisiae YOR065W   ubiquinol--cytochrome-c reductase catalytic subunit CYT1
Schistosoma japonicum Sjp_0217630   ko:K00413 ubiquinol-cytochrome c reductase cytochrome c1 subunit, putative
Schistosoma mansoni Smp_005290   cytochrome C1
Schmidtea mediterranea mk4.002563.03  
Schmidtea mediterranea mk4.002563.01   Cytochrome c1, heme protein, mitochondrial
Trypanosoma brucei gambiense Tbg972.8.1520   cytochrome c1, heme protein, mitochondrial precursor, putative
Trypanosoma brucei Tb927.8.1890   cytochrome c1, heme protein, mitochondrial, putative
Trypanosoma congolense TcIL3000_8_1840   cytochrome c1, heme protein, mitochondrial, putative
Trypanosoma cruzi TcCLB.511391.160   cytochrome c1, heme protein, mitochondrial, putative
Theileria parva TP04_0384   cytochrome c1 precursor, putative
Wolbachia endosymbiont of Brugia malayi Wbm0774   cytochrome c1

Essentiality

LmjF.07.0060 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.1890 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.8.1890 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.8.1890 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.8.1890 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C54G4.8 Caenorhabditis elegans embryonic lethal wormbase
CELE_C54G4.8 Caenorhabditis elegans larval arrest wormbase
CELE_C54G4.8 Caenorhabditis elegans larval lethal wormbase
CELE_C54G4.8 Caenorhabditis elegans slow growth wormbase
CELE_C54G4.8 Caenorhabditis elegans sterile wormbase
PBANKA_1326300 Plasmodium berghei Essential plasmo
Show/Hide essentiality data references
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

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

Druggability index (range: 0 to 1): 0.2

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

3 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.07.0060 (Leishmania major), cytochrome c1, heme protein, mitochondrial precursor, putative
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