Detailed view for LmjF.35.3840

Basic information

TDR Targets ID: 23376
Leishmania major, proteasome beta 2 subunit, putative

Source Database / ID:  TriTrypDB  GeneDB

pI: 6.9998 | Length (AA): 254 | MW (Da): 27523 | 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

PF00227   Proteasome subunit

Gene Ontology

Mouse over links to read term descriptions.
GO:0005839   proteasome core complex  
GO:0004298   threonine endopeptidase activity  
GO:0004175   endopeptidase activity  
GO:0051603   proteolysis involved in cellular protein catabolic process  

Metabolic Pathways

Proteasome (KEGG)

Structural information

Modbase 3D models:

There are 7 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
5 252 1ryp (B) 11 250 16.00 0 1 1.17 -0.88
30 213 1iru (H) 1 185 33.00 0 1 1.3 -1.53
30 250 1ryp (I) 1 222 52.00 0 1 1.59 -1.12
30 248 5le5 (H) 1 219 58.00 0 1 1.6218 -0.88
30 215 1yar (H) 1 188 27.00 0 1 1.17008 -0.89
30 253 4r17 (H) 1 225 51.00 0 1 1.53319 -0.56
31 221 5le5 (N) 2 195 32.00 0.000000000024 1 1.26497 -1.1

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_127705)

Species Accession Gene Product
Arabidopsis thaliana AT5G40580   20S proteasome beta subunit PBB2
Arabidopsis thaliana AT3G27430   20S proteasome beta subunit PBB1
Babesia bovis BBOV_IV008660   proteasome subunit beta 7, putative
Brugia malayi Bm1_30555   Proteasome A-type and B-type family protein
Candida albicans CaO19.7605   similar to S. cerevisiae PUP1 (YOR157C) proteasome subunit
Caenorhabditis elegans CELE_C47B2.4   Protein PBS-2
Cryptosporidium hominis Chro.30293   proteasome component precursor
Cryptosporidium parvum cgd3_2530   PUP1/proteasome subunit beta type 7, NTN hydrolase fold
Dictyostelium discoideum DDB_G0283679   20S proteasome subunit beta-7
Drosophila melanogaster Dmel_CG3329   Proteasome beta2 subunit
Echinococcus granulosus EgrG_000062300   proteasome subunit beta type 7
Entamoeba histolytica EHI_148040   proteasome subunit beta type 7-B precursor, putative
Echinococcus multilocularis EmuJ_000062300   proteasome subunit beta type 7
Giardia lamblia GL50803_27059   Proteasome subunit beta type 7 precursor
Homo sapiens ENSG00000136930   proteasome (prosome, macropain) subunit, beta type, 7
Leishmania braziliensis LbrM.34.3820   proteasome beta 2 subunit, putative
Leishmania donovani LdBPK_353880.1   proteasome beta 2 subunit, putative
Leishmania infantum LinJ.35.3880   proteasome beta 2 subunit, putative
Leishmania major LmjF.35.3840   proteasome beta 2 subunit, putative
Leishmania mexicana LmxM.34.3840   proteasome beta 2 subunit, putative
Loa Loa (eye worm) LOAG_05524   proteasome A-type and B-type family protein
Mus musculus ENSMUSG00000026750   proteasome (prosome, macropain) subunit, beta type 7
Neospora caninum NCLIV_053220   PsmB (EC 3.4.25.1), related
Oryza sativa 4338009   Os05g0187000
Plasmodium berghei PBANKA_1343300   proteasome subunit beta type-7, putative
Plasmodium falciparum PF3D7_1328100   proteasome subunit beta type-7, putative
Plasmodium knowlesi PKNH_1200500   proteasome subunit beta type-7, putative
Plasmodium vivax PVX_082355   proteasome subunit beta type-7, putative
Plasmodium yoelii PY04957   proteasome subunit, beta type, 7
Saccharomyces cerevisiae YOR157C   proteasome core particle subunit beta 2
Schistosoma japonicum Sjp_0002420   ko:K02739 20S proteasome subunit beta 2, putative
Schistosoma mansoni Smp_073410   proteasome catalytic subunit 2 (T01 family)
Schmidtea mediterranea mk4.000114.05   Proteasome subunit beta type
Schmidtea mediterranea mk4.000114.14   Proteasome subunit beta type
Schmidtea mediterranea mk4.000114.15   Proteasome subunit beta type
Trypanosoma brucei gambiense Tbg972.9.6750   proteasome beta 2 subunit, putative,20S proteasome subunit
Trypanosoma brucei Tb927.9.11330   proteasome beta 2 subunit, putative
Trypanosoma cruzi TcCLB.508461.430   proteasome beta 2 subunit, putative
Toxoplasma gondii TGME49_306930   proteasome subunit beta type 7 precursor, putative
Theileria parva TP01_0908   proteasome subunit beta type 7 precursor, putative
Trichomonas vaginalis TVAG_231360   Family T1, proteasome beta subunit, threonine peptidase

Essentiality

LmjF.35.3840 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.211.2590 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb09.211.2590 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb09.211.2590 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.211.2590 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C47B2.4 Caenorhabditis elegans embryonic lethal wormbase
CELE_C47B2.4 Caenorhabditis elegans larval arrest wormbase
CELE_C47B2.4 Caenorhabditis elegans larval lethal wormbase
CELE_C47B2.4 Caenorhabditis elegans slow growth wormbase
CELE_C47B2.4 Caenorhabditis elegans sterile wormbase
YOR157C Saccharomyces cerevisiae inviable yeastgenome
TGME49_306930 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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

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
Species Known druggable target Linked compounds Reference
Homo sapiens proteasome (prosome, macropain) subunit, beta type, 7 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
0.0248 0.2589 0.2837
0.0279 0.2618 0.2822
0.0178 0.2793 0.2818
0.0235 0.2697 0.2746
0.0112 0.3219 0.3399
0.0124 0.299 0.4388
0.0249 0.2605 0.2824
0.0248 0.2589 0.2837
0.0207 0.2558 0.2937
0.0231 0.3016 0.4419
0.0248 0.2589 0.2837
0.0243 0.3004 0.4419
0.0264 0.2574 0.302
0.0128 0.3001 0.4402
0.0245 0.2696 0.2741
0.0104 0.3001 0.4402
0.0118 0.3001 0.4402
0.0244 0.2619 0.282
0.0128 0.3001 0.4402
0.0248 0.2601 0.2827
0.0128 0.3016 0.4419
0.0246 0.2709 0.2749
0.0215 0.3016 0.4419
0.0236 0.3143 0.4536
0.0115 0.3216 0.3418
0.0223 0.3016 0.4419
0.024 0.2698 0.2746
0.0252 0.2576 0.3014
0.0244 0.2622 0.2814
0.0128 0.3001 0.4402
0.0238 0.3005 0.4419
0.0128 0.3001 0.4402
0.0192 0.253 0.3545
0.0128 0.3016 0.4419
0.0207 0.2558 0.2937
0.026 0.2575 0.3017
0.0258 0.2549 0.2549

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

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier LmjF.35.3840 (Leishmania major), proteasome beta 2 subunit, putative
Title for this comment
Comment