Detailed view for LmjF.28.1820

Basic information

TDR Targets ID: 29323
Leishmania major, replication factor A, 51kDa subunit, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.1847 | Length (AA): 467 | MW (Da): 52433 | 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

PF01336   OB-fold nucleic acid binding domain
PF08646   Replication factor-A C terminal domain
PF16900   Replication protein A OB domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005634   nucleus  
GO:0003677   DNA binding  
GO:0003676   nucleic acid binding  
GO:0006310   DNA recombination  
GO:0006281   DNA repair  
GO:0006260   DNA replication  

Structural information

Modbase 3D models:

There are 9 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
6 120 1ynx (A) 181 294 36.00 0 1 0.72 -1.06
8 248 1jmc (A) 183 419 41.00 0 1 1.09 -0.95
141 248 1o7i (A) 10 115 25.00 0.000016 0.77 0.56 -0.63
271 453 1l1o (C) 439 611 31.00 0 1 0.67 0.06
6 113 3u4v (A) 210 308 27.00 0 0.98 0.553163 -0.78
8 249 1jmc (A) 183 420 40.00 0 1 1.0264 -0.4
9 435 4gnx (C) 182 607 33.00 0 1 1.24155 0.41
9 453 4gnx (C) 182 620 28.00 0 1 1.21679 0.53
134 216 2k50 (A) 7 90 27.00 0.26 0.62 0.45953 0.15

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 60-80% percentile metacyclic. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile amastigotes. 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_127539)

Species Accession Gene Product
Arabidopsis thaliana AT5G45400   replication protein RPA70C
Arabidopsis thaliana AT2G06510   replication factor A 1A
Arabidopsis thaliana AT5G61000   replication protein A 70 kDa DNA-binding subunit D
Arabidopsis thaliana AT5G08020   RPA70-kDa subunit B
Arabidopsis thaliana AT4G19130   Replication factor-A protein 1-related
Babesia bovis BBOV_III010480   replication factor-a protein 1 (rpa1) family protein
Brugia malayi Bm1_18390   replication factor A 73 kDa subunit
Candida albicans CaO19.2093   similar to single-stranded DNA binding protein involved in DNA-damage repair
Candida albicans CaO19.9640   similar to single-stranded DNA binding protein involved in DNA-damage repair
Caenorhabditis elegans CELE_F18A1.5   Protein RPA-1
Cryptosporidium hominis Chro.70509   replication protein A 70kDa
Cryptosporidium parvum cgd7_4620   Rf-A (OB fold protein)
Dictyostelium discoideum DDB_G0289513   OB fold-containing protein, nucleic acid binding
Drosophila melanogaster Dmel_CG9633   Replication Protein A 70
Echinococcus granulosus EgrG_000714700   replication protein A 70 kDa DNA binding
Entamoeba histolytica EHI_062980   replication factor A protein 1, putative
Echinococcus multilocularis EmuJ_000714700   replication protein A 70 kDa DNA binding
Homo sapiens ENSG00000132383   replication protein A1, 70kDa
Leishmania braziliensis LbrM.28.1990   replication factor A, 51kDa subunit, putative
Leishmania donovani LdBPK_281940.1   Replication factor A protein 1
Leishmania infantum LinJ.28.1940   replication factor A, 51kDa subunit, putative
Leishmania major LmjF.28.1820   replication factor A, 51kDa subunit, putative
Leishmania mexicana LmxM.28.1820   replication factor A, 51kDa subunit, putative
Loa Loa (eye worm) LOAG_09949   replication factor A 73 kDa subunit
Mus musculus ENSMUSG00000000751   replication protein A1
Neospora caninum NCLIV_050400   hypothetical protein
Oryza sativa 4330902   Os02g0776800
Oryza sativa 4332052   Os03g0214100
Oryza sativa 4337594   Os05g0111000
Onchocerca volvulus OVOC9194   Putative replication factor A 73 kDa subunit
Plasmodium berghei PBANKA_1007200   replication protein A1, large subunit, putative
Plasmodium falciparum PF3D7_0409600   replication protein A1, large subunit
Plasmodium knowlesi PKNH_0307700   replication protein A1, large subunit, putative
Plasmodium vivax PVX_000765   replication protein A1, large subunit, putative
Plasmodium yoelii PY04090   putative replication A protein
Saccharomyces cerevisiae YAR007C   Rfa1p
Schistosoma japonicum Sjp_0015650   ko:K07466 replication factor A1, putative
Schistosoma mansoni Smp_121800   replication factor A 1 rfa1
Schmidtea mediterranea mk4.003115.03  
Schmidtea mediterranea mk4.003115.02  
Schmidtea mediterranea mk4.003630.01  
Trypanosoma brucei gambiense Tbg972.11.10200   replication factor A, 51kDa subunit, putative
Trypanosoma brucei Tb927.11.9130   Replication factor A protein 1
Trypanosoma congolense TcIL3000.11.9490   Replication factor A protein 1
Trypanosoma cruzi TcCLB.510901.60   Replication factor A protein 1
Toxoplasma gondii TGME49_236080   replication factor-a protein 1 (rpa1) subfamily protein
Theileria parva TP02_0095   replication factor A protein, putative
Trichomonas vaginalis TVAG_060460   replication factor A 1, rfa1, putative
Trichomonas vaginalis TVAG_226230   replication factor A 1, rfa1, putative
Trichomonas vaginalis TVAG_294830   replication factor A 1, rfa1, putative
Trichomonas vaginalis TVAG_433860   replication factor A 1, rfa1, putative

Essentiality

LmjF.28.1820 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.0870 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.01.0870 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.0870 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.01.0870 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F18A1.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_F18A1.5 Caenorhabditis elegans sterile wormbase
YAR007C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1007200 Plasmodium berghei Slow plasmo
TGME49_236080 Toxoplasma gondii Probably essential sidik
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
  • 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
  • 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.
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
Species Known druggable target Linked compounds Reference
Homo sapiens replication protein A1, 70kDa 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
0.0422 0.4736 1
0.0326 0.3476 1
0.0423 0.4678 1
0.0084 0.4182 1
0.047 0.2769 1
0.005 0.3476 0.5
0.0137 0.3901 0.5
0.0066 0.3901 0.5
0.043 0.2563 1
0.0024 0.277 0.5
0.0431 0.4678 1
0.0187 0.418 1
0.0092 0.3901 0.5
0.0148 0.3476 0.5
0.0399 0.4182 0.5
0.0151 0.3901 0.5
0.0364 0.4659 1
0.0058 0.3476 0.5
0.0502 0.437 0.5
0.0182 0.4234 0.5
0.0094 0.3901 0.5
0.0165 0.4234 0.5
0.0165 0.4085 0.5
0.0423 0.4732 1
0.0433 0.4678 1
0.0091 0.3901 0.5
0.0182 0.4234 0.5
0.0059 0.4181 0.5
0.0086 0.3046 1
0.0405 0.4734 1
0.0326 0.3476 1
0.048 0.4596 1
0.0199 0.4234 0.5

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.28.1820 (Leishmania major), replication factor A, 51kDa subunit, putative
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