Detailed view for LmjF.25.0740

Basic information

TDR Targets ID: 28695
Leishmania major, DNA repair protein, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.4194 | Length (AA): 1092 | MW (Da): 122535 | 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

PF00176   SNF2 family N-terminal domain
PF00271   Helicase conserved C-terminal domain
PF00645   Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
PF13639   Ring finger domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0003676   nucleic acid binding  
GO:0008270   zinc ion binding  
GO:0005524   ATP binding  
GO:0005515   protein binding  
GO:0004386   helicase activity  
GO:0003677   DNA binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 12 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
915 1062 1t5i (A) 263 406 20.00 0.0000065 1 0.52 -1.28
917 1091 1z5z (A) 724 900 28.00 0 1 0.52 -0.86
19 127 2cs2 (A) 7 122 21.00 0 0.86 0.321617 -0.03
29 113 1v9x (A) 10 92 22.00 0 0.75 0.365639 -0.3
123 263 5hzr (A) 529 674 38.00 0.000000015 0.83 0.392321 0.4
564 1087 1z63 (A) 554 896 33.00 0 1 0.159053 1.81
789 851 5d1m (B) 133 217 33.00 0.25 0.99 0.438892 -0.72
790 835 3asl (A) 317 363 35.00 0 0.94 0.457925 -0.07
791 843 5d0i (B) 294 342 45.00 0.11 0.87 0.427735 0.28
791 845 4ccg (X) 307 370 29.00 0 1 0.204166 -0.27
925 1062 1t5i (A) 274 406 20.00 0 1 0.467174 -0.92
927 989 2dgp (A) 52 118 41.00 0.24 0.4 0.284892 0.83

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_130425)

Species Accession Gene Product
Arabidopsis thaliana AT1G05120   Helicase protein with RING/U-box domain
Babesia bovis BBOV_III008700   DNA repair protein rhp16, putative
Candida albicans CaO19.10486   similar to S. cerevisiae repairosome nucleotide excision repair protein (SNF helicase domain)
Candida albicans CaO19.2969   similar to S. cerevisiae repairosome nucleotide excision repair protein (SNF helicase domain)
Cryptosporidium hominis Chro.40028   DNA repair protein rhp16
Cryptosporidium parvum cgd4_140   Swi2/Snf2 ATpase,Rad16 ortholog
Leishmania braziliensis LbrM.25.0620   DNA repair protein, putative
Leishmania donovani LdBPK_250770.1   DNA repair protein, putative
Leishmania infantum LinJ.25.0770   DNA repair protein, putative
Leishmania major LmjF.25.0740   DNA repair protein, putative
Leishmania mexicana LmxM.25.0740   DNA repair protein, putative
Neospora caninum NCLIV_046520   hypothetical protein
Oryza sativa 4343361   Os07g0511500
Plasmodium berghei PBANKA_1463700   DNA repair protein rhp16, putative
Plasmodium falciparum PF3D7_1250800   DNA repair protein rhp16, putative
Plasmodium knowlesi PKNH_1470800   DNA repair protein rhp16, putative
Plasmodium vivax PVX_101435   DNA repair protein rhp16, putative
Plasmodium yoelii PY00648   similar nucleotide excision repair proteins-related
Plasmodium yoelii PY01231   SNF2 family N-terminal domain, putative
Saccharomyces cerevisiae YBR114W   DNA repair protein RAD16
Trypanosoma brucei gambiense Tbg972.11.750   DNA repair protein, putative
Trypanosoma brucei Tb927.11.750   DNA repair protein, putative
Trypanosoma congolense TcIL3000_0_15260   DNA repair protein, putative
Trypanosoma cruzi TcCLB.506925.140   DNA repair protein, putative
Toxoplasma gondii TGME49_226440   SWI2/SNF2-containing protein RAD16

Essentiality

LmjF.25.0740 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.03.0400 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.03.0400 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb11.03.0400 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.03.0400 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
PBANKA_1463700 Plasmodium berghei Dispensable plasmo
TGME49_226440 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • 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
  • 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
  • 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.
  • 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
  • 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
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.

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.25.0740 (Leishmania major), DNA repair protein, putative
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