Detailed view for LmjF.25.0080

Basic information

TDR Targets ID: 27667
Leishmania major, poly(A)-binding protein 3
Source Database / ID:  TriTrypDB  GeneDB

pI: 9.1533 | Length (AA): 544 | MW (Da): 60900 | Paralog Number: 1

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

PF00076   RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF00658   Poly-adenylate binding protein, unique domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0003676   nucleic acid binding  
GO:0000166   nucleotide binding  
GO:0003723   RNA 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
101 369 2ghp (A) 43 290 30.00 0.0000000039 1 0.62 0.34
291 349 1x4e (A) 8 67 34.00 0.0000077 1 0.72 -1.99
293 422 2adc (A) 341 466 20.00 0.00000036 0.97 0.46 0
439 541 1g9l (A) 17 125 37.00 0.0000000017 1 0.62 -0.25
483 541 1i2t (A) 1010 1068 37.00 0.000000000011 1 0.86 -2.99
5 35 2cpj (A) 70 98 38.00 0.11 0.23 0.356285 0.21
9 181 4f02 (A) 12 181 51.00 0 1 0.989215 -0.91
94 397 4n0t (A) 36 318 27.00 0 1 0.705024 0.84
289 354 2x1f (A) 18 84 32.00 0.00016 1 0.699524 -1.78
418 543 1g9l (A) 11 127 33.00 0 1 0.534918 0.34
474 541 1nmr (A) 15 82 51.00 0.00000000014 0.5 0.6312 0.44
483 541 1i2t (A) 1010 1068 37.00 0 1 0.663956 -1.31

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_126795)

Species Accession Gene Product
Arabidopsis thaliana AT2G23350   poly(A) binding protein 4
Arabidopsis thaliana AT1G22760   polyadenylate-binding protein 3
Arabidopsis thaliana AT1G49760   poly(A) binding protein 8
Arabidopsis thaliana AT4G34110   polyadenylate-binding protein 2
Arabidopsis thaliana AT1G71770   polyadenylate-binding protein 5
Babesia bovis BBOV_IV008280   polyadenylate binding protein, putative
Brugia malayi Bm1_06880   polyadenylate-binding protein 4
Brugia malayi Bm1_16080   polyadenylate-binding protein 1
Candida albicans CaO19.3037   similar to PolyA Binding Protein
Candida albicans CaO19.10555   similar to PolyA Binding Protein
Caenorhabditis elegans CELE_F18H3.3   Protein PAB-2, isoform B
Caenorhabditis elegans CELE_Y106G6H.2   Protein PAB-1, isoform B
Cryptosporidium hominis Chro.60347   poly(a)-binding protein fabm
Cryptosporidium parvum cgd6_3010   poly(a)-binding protein fabm, putative
Dictyostelium discoideum DDB_G0290745   RNA recognition motif-containing protein RRM
Dictyostelium discoideum DDB_G0293558   RNA recognition motif-containing protein RRM
Drosophila melanogaster Dmel_CG5119   CG5119 gene product from transcript CG5119-RC
Echinococcus granulosus EgrG_000689000   polyadenylate binding protein
Entamoeba histolytica EHI_033250   polyadenylate-binding protein, putative
Entamoeba histolytica EHI_198750   polyadenylate-binding protein, putative
Echinococcus multilocularis EmuJ_000689000   polyadenylate binding protein
Giardia lamblia GL50803_5942   Polyadenylate-binding protein, putative
Homo sapiens ENSG00000090621   poly(A) binding protein, cytoplasmic 4 (inducible form)
Homo sapiens 5042   poly(A) binding protein, cytoplasmic 3
Homo sapiens ENSG00000070756   poly(A) binding protein, cytoplasmic 1
Homo sapiens ENSG00000101104   poly(A) binding protein, cytoplasmic 1-like
Homo sapiens 100996696   polyadenylate-binding protein 4-like
Leishmania braziliensis LbrM.34.4130   poly(A)-binding protein 2, putative;with=GeneDB:LmjF35.4130,poly(A)-binding protein 2, putative
Leishmania braziliensis LbrM.25.0080   poly(A)-binding protein 3, putative;with=GeneDB:LmjF25.0080
Leishmania braziliensis LbrM.34.4980   polyadenylate-binding protein 1, putative
Leishmania donovani LdBPK_354200.1   polyadenylate-binding protein 2
Leishmania donovani LdBPK_355360.1   polyadenylate-binding protein 1, putative
Leishmania donovani LdBPK_250080.1   poly(A)-binding protein, putative
Leishmania infantum LinJ.25.0080   poly(A)-binding protein 3, putative;with=GeneDB:LmjF25.0080
Leishmania infantum LinJ.35.4200   poly(A)-binding protein 2,poly(a) binding protein, putative
Leishmania infantum LinJ.35.5360   polyadenylate-binding protein 1, putative
Leishmania major LmjF.25.0080   poly(A)-binding protein 3
Leishmania major LmjF.35.4130   poly(A)-binding protein 2
Leishmania mexicana LmxM.34.4130   poly(a) binding protein, putative
Leishmania mexicana LmxM.25.0080   poly(A)-binding protein, putative
Loa Loa (eye worm) LOAG_01058   hypothetical protein
Mus musculus ENSMUSG00000046173   poly(A) binding protein, cytoplasmic 6
Mus musculus ENSMUSG00000011257   poly(A) binding protein, cytoplasmic 4
Mus musculus ENSMUSG00000054582   poly(A) binding protein, cytoplasmic 1-like
Mus musculus ENSMUSG00000022283   poly(A) binding protein, cytoplasmic 1
Mus musculus ENSMUSG00000051732   poly(A) binding protein, cytoplasmic 2
Neospora caninum NCLIV_047860   hypothetical protein
Oryza sativa 4336331   Os04g0504800
Oryza sativa 4345242   Os08g0314800
Oryza sativa 4346409   Os09g0115400
Plasmodium berghei PBANKA_1439200   polyadenylate-binding protein, putative
Plasmodium falciparum PF3D7_1224300   polyadenylate-binding protein, putative
Plasmodium knowlesi PKNH_1443600   polyadenylate-binding protein, putative
Plasmodium vivax PVX_123845   polyadenylate-binding protein, putative
Plasmodium yoelii PY05398   polyA binding protein-related
Saccharomyces cerevisiae YER165W   polyadenylate-binding protein
Schistosoma japonicum Sjp_0054250   Embryonic polyadenylate-binding protein, putative
Schistosoma mansoni Smp_024140.4   polyadenylate binding protein
Schistosoma mansoni Smp_024140.1   polyadenylate binding protein
Schistosoma mansoni Smp_024140.3   polyadenylate binding protein
Schmidtea mediterranea mk4.000447.00  
Schmidtea mediterranea mk4.000416.00  
Schmidtea mediterranea mk4.004061.04   Polyadenylate-binding protein
Schmidtea mediterranea mk4.003215.02  
Schmidtea mediterranea mk4.006385.02  
Schmidtea mediterranea mk4.003818.00   Polyadenylate-binding protein
Schmidtea mediterranea mk4.002124.05  
Schmidtea mediterranea mk4.005479.01  
Schmidtea mediterranea mk4.000416.02  
Schmidtea mediterranea mk4.010078.00   Polyadenylate-binding protein
Schmidtea mediterranea mk4.000989.04  
Schmidtea mediterranea mk4.007846.00   Polyadenylate-binding protein
Schmidtea mediterranea mk4.000390.12  
Schmidtea mediterranea mk4.000374.03  
Schmidtea mediterranea mk4.000625.04  
Schmidtea mediterranea mk4.005479.02  
Schmidtea mediterranea mk4.001814.01  
Schmidtea mediterranea mk4.005746.01  
Schmidtea mediterranea mk4.000488.04  
Schmidtea mediterranea mk4.019643.00   Polyadenylate-binding protein
Schmidtea mediterranea mk4.001659.01  
Trypanosoma brucei gambiense Tbg972.9.6330   poly(A)-binding protein 1,PABP2
Trypanosoma brucei gambiense Tbg972.9.5210   polyadenylate-binding protein 1, putative,PABP1
Trypanosoma brucei Tb927.9.10770   polyadenylate-binding protein 2
Trypanosoma brucei Tb927.9.9290   polyadenylate-binding protein 1
Trypanosoma congolense TcIL3000_9_3370   polyadenylate-binding protein 1, putative
Trypanosoma congolense TcIL3000_9_4350   polyadenylate-binding protein 2
Trypanosoma cruzi TcCLB.506885.70   polyadenylate-binding protein 1, putative
Trypanosoma cruzi TcCLB.508461.140   polyadenylate-binding protein, putative
Toxoplasma gondii TGME49_224850   polyadenylate binding protein, putative
Theileria parva TP01_0945   polyadenylate binding protein, putative
Trichomonas vaginalis TVAG_278520   polyadenylate-binding protein, putative
Trichomonas vaginalis TVAG_353810   RNA-binding protein, putative
Trichomonas vaginalis TVAG_357520   nuclear acid binding protein, putative
Trichomonas vaginalis TVAG_385330   RNA-binding protein, putative
Trichomonas vaginalis TVAG_371230   poly(A) binding protein, putative
Trichomonas vaginalis TVAG_371220   ribonucleoprotein, chloroplast, putative

Essentiality

LmjF.25.0080 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.0930 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb09.211.0930 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.211.0930 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb09.211.0930 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Tb09.211.2150 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb09.211.2150 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.211.2150 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb09.211.2150 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y106G6H.2 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y106G6H.2 Caenorhabditis elegans larval arrest wormbase
CELE_Y106G6H.2 Caenorhabditis elegans slow growth wormbase
CELE_Y106G6H.2 Caenorhabditis elegans sterile wormbase
CELE_F18H3.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_F18H3.3 Caenorhabditis elegans sterile wormbase
YER165W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1439200 Plasmodium berghei Essential plasmo
TGME49_224850 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • 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

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 poly(A) binding protein, cytoplasmic 1 Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

No enough druggable targets predicted through repurposing network model to make a plot

Putative Drugs List

Compound Raw Global Species
0.0007 0.5764 0

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.

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Gene identifier LmjF.25.0080 (Leishmania major), poly(A)-binding protein 3
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