Detailed view for LmjF.16.1320

Basic information

TDR Targets ID: 29788
Leishmania major, cytochrome c, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 10.1863 | Length (AA): 113 | MW (Da): 12188 | Paralog Number: 1

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

PF00034   Cytochrome c

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

This gene is not mapped to any metabolic pathway in 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
3 113 1ytc () 0 102 46.00 0 1 1.61 -1.09
10 113 1hro (A) 4 106 55.00 0 1 1.67 -1.18
12 112 5cyt (R) 1 101 52.00 0 1 1.57 -1.24

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:

PDB tag
  • 4DY9:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4GED:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 60-80% 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_127365)

Species Accession Gene Product
Arabidopsis thaliana AT4G10040   cytochrome c-2
Babesia bovis BBOV_III005520   cytochrome c, putative
Brugia malayi Bm1_28235   Cytochrome c type-1
Candida albicans CaO19.1770   cytochrome c capable of functionally substituting for S. cerevisiae CYC1 (YJR048W) mitochondrial iso-1-cytochrome c
Candida albicans CaO19.9339   cytochrome c capable of functionally substituting for S. cerevisiae CYC1 (YJR048W) mitochondrial iso-1-cytochrome c
Caenorhabditis elegans CELE_E04A4.7   Protein CYC-2.1
Caenorhabditis elegans CELE_ZC116.2   Protein CYC-2.2
Dictyostelium discoideum DDB_G0275537   cytochrome c
Drosophila melanogaster Dmel_CG13263   Cytochrome c distal
Drosophila melanogaster Dmel_CG17903   Cytochrome c proximal
Echinococcus granulosus EgrG_000340200   cytochrome c
Echinococcus multilocularis EmuJ_000340200   cytochrome c
Homo sapiens 54205   cytochrome c, somatic
Leishmania braziliensis LbrM.16.1360   cytochrome c, putative
Leishmania braziliensis LbrM.16.1370   cytochrome c, putative
Leishmania donovani LdBPK_161390.1   cytochrome c, putative
Leishmania donovani LdBPK_161380.1   cytochrome c, putative
Leishmania infantum LinJ.16.1390   cytochrome c, putative
Leishmania infantum LinJ.16.1380   cytochrome c, putative
Leishmania major LmjF.16.1320   cytochrome c, putative
Leishmania major LmjF.16.1310   cytochrome c, putative
Leishmania mexicana LmxM.16.1320   cytochrome c, putative
Leishmania mexicana LmxM.16.1310   cytochrome c, putative
Loa Loa (eye worm) LOAG_05968   cytochrome c type-1
Mus musculus ENSMUSG00000063694   cytochrome c, somatic
Mus musculus ENSMUSG00000056436   cytochrome c, testis
Neospora caninum NCLIV_060860   Cytochrome c, related
Oryza sativa 4338825   Os05g0420600
Plasmodium berghei PBANKA_1038000   cytochrome c, putative
Plasmodium falciparum PF3D7_1404100   cytochrome c, putative
Plasmodium knowlesi PKNH_1354000   cytochrome c, putative
Plasmodium vivax PVX_086230   cytochrome c, putative
Plasmodium yoelii PY05430   cytochrome c
Saccharomyces cerevisiae YJR048W   cytochrome c isoform 1
Saccharomyces cerevisiae YEL039C   cytochrome c isoform 2
Schistosoma japonicum Sjp_0206780   ko:K08738 cytochrome c, putative
Schistosoma mansoni Smp_033400   cytochrome c
Schmidtea mediterranea mk4.002115.02   Cytochrome c
Schmidtea mediterranea mk4.001008.09   Cytochrome c
Trypanosoma brucei gambiense Tbg972.8.4960   cytochrome c
Trypanosoma brucei Tb927.8.5120   cytochrome c
Trypanosoma congolense TcIL3000_8_4910   cytochrome c, putative
Trypanosoma cruzi TcCLB.508959.4   cytochrome c, putative
Trypanosoma cruzi TcCLB.506949.50   cytochrome c, putative
Toxoplasma gondii TGME49_219750   cytochrome c, putative
Theileria parva TP02_0396   cytochrome c, putative
Wolbachia endosymbiont of Brugia malayi Wbm0123   cytochrome c2

Essentiality

LmjF.16.1320 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.5120 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.8.5120 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.8.5120 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.8.5120 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_ZC116.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_ZC116.2 Caenorhabditis elegans slow growth wormbase
CELE_E04A4.7 Caenorhabditis elegans embryonic lethal wormbase
CELE_E04A4.7 Caenorhabditis elegans larval arrest wormbase
CELE_E04A4.7 Caenorhabditis elegans larval lethal wormbase
CELE_E04A4.7 Caenorhabditis elegans slow growth wormbase
CELE_E04A4.7 Caenorhabditis elegans sterile wormbase
PBANKA_1038000 Plasmodium berghei Essential plasmo
TGME49_219750 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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.
  • 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
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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
Species Known druggable target Linked compounds Reference
Homo sapiens cytochrome c, somatic Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.01 0.2631 1
0.0133 0.2756 0.5
0.0102 0.2905 0.3945
0.0032 0.2662 0.5
0.0032 0.2662 0.5
0.0102 0.2905 0.3945
0.01 0.2997 0.5
0.0138 0.3485 1
0.0138 0.2714 0.5
0.0032 0.2662 0.5
0.01 0.2631 1

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 LmjF.16.1320 (Leishmania major), cytochrome c, putative
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