Detailed view for LmjF.21.1330

Basic information

TDR Targets ID: 25550
Leishmania major, hypothetical protein, conserved
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.3043 | Length (AA): 1592 | MW (Da): 177249 | 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

PF02463   RecF/RecN/SMC N terminal domain
PF06470   SMC proteins Flexible Hinge Domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005694   chromosome  
GO:0005524   ATP binding  
GO:0005515   protein binding  
GO:0051276   chromosome organization and biogenesis  

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
174 348 1e69 (A) 1 1035 29.00 0.0000000000031 0.76 0.17 0.58
376 1179 1tr2 (A) 145 970 10.00 0 1 0.15 0.97
684 863 1gxj (A) 499 657 23.00 0.0000023 1 0.27 -0.31
1261 1474 1w1w (A) 102 1223 30.00 0 0.87 0.34 0.18
1328 1457 1xew (Y) 1013 1143 42.00 0 1 0.77 -1.74
174 285 4i99 (A) 2 115 29.00 0.00022 0.6 0.399152 -0.13
176 356 3kta (A) 4 168 36.00 0 0.82 0.386893 0.28
179 226 1w1w (B) 7 54 48.00 0.044 0.73 0.527951 0.31
427 580 4uos (A) 9 182 26.00 0.11 0.91 0.254934 -0.48
548 1281 1tr2 (A) 149 968 23.00 0.015 1 0.450255 1.3
879 1067 4uos (A) 1 183 8.00 0 0.03 0.213819 -1.25
1297 1469 1w1w (B) 180 1216 39.00 0 1 0.536868 0.01

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
Lower 20-40% 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_127440)

Species Accession Gene Product
Arabidopsis thaliana AT5G48600   structural maintenance of chromosomes protein 4
Babesia bovis BBOV_III010300   SMC family, C-terminal domain containing protein
Brugia malayi Bm1_07830   SMC family, C-terminal domain containing protein
Candida albicans CaO19.8579   potential SMC chromosomal ATPase similar to S. cerevisiae SMC4 (YLR086W) nuclear condensin complex ATPase
Candida albicans CaO19.964   potential SMC chromosomal ATPase similar to S. cerevisiae SMC4 (YLR086W) nuclear condensin complex ATPase
Caenorhabditis elegans CELE_F35G12.8   Protein SMC-4
Caenorhabditis elegans CELE_R13G10.1   Protein DPY-27
Cryptosporidium hominis Chro.70215   stable maintenance of chromosomes; Smc4p
Cryptosporidium parvum cgd7_1850   SMC4SMC4, chromosomal ATpase with giant coiled coil regions
Dictyostelium discoideum DDB_G0286403   structural maintenance of chromosome protein
Drosophila melanogaster Dmel_CG11397   gluon
Echinococcus granulosus EgrG_000517500   structural maintenance of chromosomes protein
Entamoeba histolytica EHI_199700   SMC4 protein, putative
Echinococcus multilocularis EmuJ_000517500   structural maintenance of chromosomes protein
Giardia lamblia GL50803_17465   SMC4-like protein
Homo sapiens ENSG00000113810   structural maintenance of chromosomes 4
Leishmania braziliensis LbrM.21.1570   hypothetical protein, conserved
Leishmania donovani LdBPK_211580.1   RecF/RecN/SMC N terminal domain/SMC proteins Flexible Hinge Domain, putative
Leishmania infantum LinJ.21.1580   hypothetical protein, conserved
Leishmania major LmjF.21.1330   hypothetical protein, conserved
Leishmania mexicana LmxM.21.1330partial   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_02100   hypothetical protein
Loa Loa (eye worm) LOAG_10473   hypothetical protein
Loa Loa (eye worm) LOAG_10474   Smc4l1 protein
Mycobacterium leprae ML1629c   PROBABLE CHROMOSOME PARTITION PROTEIN SMC
Mus musculus ENSMUSG00000034349   structural maintenance of chromosomes 4
Neospora caninum NCLIV_031540   chromosome condensation protein, putative
Oryza sativa 9267154   Os05g0497100
Onchocerca volvulus OVOC2348  
Plasmodium berghei PBANKA_1108700   structural maintenance of chromosomes protein 4, putative
Plasmodium falciparum PF3D7_0509100   structural maintenance of chromosomes protein 4, putative
Plasmodium knowlesi PKNH_1024500   structural maintenance of chromosomes protein 4, putative
Plasmodium vivax PVX_098020   chromosome condensation protein, putative
Plasmodium yoelii PY03258   chromosome assembly protein xcap-c
Saccharomyces cerevisiae YLR086W   condensin subunit SMC4
Schistosoma japonicum Sjp_0302410   ko:K06675 structural maintenance of chromosome 4, putative
Schistosoma japonicum Sjp_0084840   ko:K06675 structural maintenance of chromosome 4, putative
Schistosoma mansoni Smp_173700   chondroitin sulfate proteoglycan
Schmidtea mediterranea mk4.000285.04   Structural maintenance of chromosomes protein 4
Schmidtea mediterranea mk4.000285.05  
Trypanosoma brucei gambiense Tbg972.10.760   structural maintenance of chromosome 4, putative
Trypanosoma brucei Tb927.10.740   structural maintenance of chromosome 4, putative
Trypanosoma brucei Tb11.v5.0750   dual specificity protein phosphatase, putative
Trypanosoma brucei Tb11.v5.0749   structural maintenance of chromosome 4, putative
Trypanosoma congolense TcIL3000_10_600   structural maintenance of chromosome 4, putative
Trypanosoma cruzi TcCLB.506855.90   structural maintenance of chromosome protein 4, putative
Trypanosoma cruzi TcCLB.508779.90   structural maintenance of chromosome protein 4, putative
Toxoplasma gondii TGME49_231170   RecF/RecN/SMC N terminal domain-containing protein
Treponema pallidum TP0367   chromosome segregation protein
Theileria parva TP02_0117   hypothetical protein
Trichomonas vaginalis TVAG_160280   condensin subunit Smc4
Trichomonas vaginalis TVAG_434480   condensin subunit Smc4

Essentiality

LmjF.21.1330 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.740 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.740 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.740 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.740 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_R13G10.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_R13G10.1 Caenorhabditis elegans larval arrest wormbase
CELE_R13G10.1 Caenorhabditis elegans slow growth wormbase
CELE_F35G12.8 Caenorhabditis elegans embryonic lethal wormbase
CELE_F35G12.8 Caenorhabditis elegans larval arrest wormbase
YLR086W Saccharomyces cerevisiae inviable yeastgenome
TGME49_231170 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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
  • 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
  • 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

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
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.21.1330 (Leishmania major), hypothetical protein, conserved
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