Detailed view for LmjF.34.2830

Basic information

TDR Targets ID: 29562
Leishmania major, ubiquitin related modifier (urm1)-like protein
Source Database / ID:  TriTrypDB  GeneDB

pI: 4.4158 | Length (AA): 103 | MW (Da): 11101 | Paralog Number: 0

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

PF09138   Urm1 (Ubiquitin related modifier)

Gene Ontology

Mouse over links to read term descriptions.
GO:0034227   tRNA thio-modification  
GO:0005737   cytoplasm  

Metabolic Pathways

Sulfur relay system (KEGG)

Structural information

Modbase 3D models:

There are 5 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
8 103 2ax5 (A) 4 99 34.00 0 1 1.43 -0.72
8 103 1wgk (A) 14 108 45.00 0 1 1.58 -1.55
5 103 2k9x (A) 4 102 59.00 0 1 1.64927 -0.09
7 103 1wgk (A) 13 108 44.00 0 1 1.50785 -1.07
35 103 4n6e (B) 25 90 30.00 0.42 0.99 1.063 -0.45

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. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile 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_128383)

Species Accession Gene Product
Arabidopsis thaliana AT2G45695   ubiquitin-related modifier 1-1
Arabidopsis thaliana AT3G61113   ubiquitin-related modifier 1
Babesia bovis BBOV_I000750   conserved hypothetical protein
Brugia malayi Bm1_03105   Hypothetical 11.0 kDa protein in FAA3-MAS3 intergenic region
Candida albicans CaO19.9835   ubiquitin related modifier
Candida albicans CaO19.2299   ubiquitin related modifier
Candida albicans CaO19.1016   similar to Ubiquitin Related Modifier
Caenorhabditis elegans CELE_F43D9.6   Protein URM-1
Cryptosporidium hominis Chro.70369   chromosome 9 open reading frame 74
Cryptosporidium parvum cgd7_3310   hypothetical protein
Dictyostelium discoideum DDB_G0283737   hypothetical protein
Drosophila melanogaster Dmel_CG33276   CG33276 gene product from transcript CG33276-RB
Echinococcus granulosus EgrG_000986700   Ubiquitin modifier 1 protein
Entamoeba histolytica EHI_010030   hypothetical protein
Echinococcus multilocularis EmuJ_000986700   Ubiquitin modifier 1 protein
Giardia lamblia GL50803_11884   Hypothetical protein
Homo sapiens ENSG00000167118   ubiquitin related modifier 1
Leishmania braziliensis LbrM.20.2450   ubiquitin related modifier (urm1)-like protein
Leishmania donovani LdBPK_342690.1   ubiquitin related modifier (urm1)-like protein
Leishmania infantum LinJ.34.2690   ubiquitin related modifier (urm1)-like protein
Leishmania major LmjF.34.2830   ubiquitin related modifier (urm1)-like protein
Leishmania mexicana LmxM.33.2830   ubiquitin related modifier (urm1)-like protein
Loa Loa (eye worm) LOAG_01612   hypothetical protein
Mus musculus ENSMUSG00000069020   ubiquitin related modifier 1 homolog (S. cerevisiae)
Oryza sativa 4343175   Os07g0466300
Plasmodium berghei PBANKA_0910600   ubiquitin-related modifier 1, putative
Plasmodium falciparum PF3D7_1138100   ubiquitin-related modifier 1, putative
Plasmodium knowlesi PKNH_0936300   ubiquitin-related modifier 1, putative
Plasmodium vivax PVX_092520   ubiquitin-related modifier 1, putative
Plasmodium yoelii PY06420   Oryza sativa Rurm1-related
Saccharomyces cerevisiae YIL008W   ubiquitin-related modifier URM1
Schistosoma japonicum Sjp_0070060   ko:K01312 trypsin [EC3.4.21.4], putative
Schistosoma mansoni Smp_030180   hypothetical protein
Schmidtea mediterranea mk4.001512.01   Ubiquitin-related modifier 1 homolog
Trypanosoma brucei gambiense Tbg972.4.1740   hypothetical protein, conserved
Trypanosoma brucei Tb927.4.1830   Urm1 (Ubiquitin related modifier), putative
Trypanosoma congolense TcIL3000_4_1480   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.510879.60   Urm1 (Ubiquitin related modifier), putative
Trypanosoma cruzi TcCLB.504013.55   Urm1 (Ubiquitin related modifier), putative
Theileria parva TP02_0852   hypothetical protein
Trichomonas vaginalis TVAG_319610   conserved hypothetical protein

Essentiality

LmjF.34.2830 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.1830 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.1830 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.4.1830 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.4.1830 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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
  • 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.
  • 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
  • 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.
  • 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
  • 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
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

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

Enter your comment

User ()
Gene identifier LmjF.34.2830 (Leishmania major), ubiquitin related modifier (urm1)-like protein
Title for this comment
Comment