Detailed view for Rv2559c

Basic information

TDR Targets ID: 8609
Mycobacterium tuberculosis, Conserved hypothetical alanine leucine valine rich protein
Source Database / ID:  Tuberculist 

pI: 6.6447 | Length (AA): 452 | MW (Da): 47499 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | 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

PF00004   ATPase family associated with various cellular activities (AAA)
PF12002   MgsA AAA+ ATPase C terminal
PF16193   AAA C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0017111   nucleoside-triphosphatase activity  
GO:0005524   ATP binding  
GO:0003824   catalytic activity  
GO:0003677   DNA binding  
GO:0000166   nucleotide binding  
GO:0006260   DNA replication  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 4 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
29 449 3pvs (A) 14 440 42.00 0 1 1.32602 0.54
30 232 1iqp (A) 14 216 31.00 0.00000000031 1 0.759815 0.11
68 171 4lcb (A) 131 257 29.00 0.01 0.85 0.560789 -0.24
262 444 3bge (A) 251 434 49.00 0 1 0.835567 0.31

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
Upper 80-100% percentile Dormant phase. murphy
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Dormant phase. hasan
Show/Hide expression data references
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.

Orthologs

Ortholog group members (OG5_128067)

Species Accession Gene Product
Arabidopsis thaliana AT1G24290   AAA-type ATPase-like protein
Candida albicans CaO19.3019   similar to subunits E. coli DNA polymerase III
Candida albicans CaO19.10537   similar to subunits E. coli DNA polymerase III
Dictyostelium discoideum DDB_G0272158   hypothetical protein
Escherichia coli b0892   DNA-dependent ATPase involved in processing recombination intermediates at replication forks
Entamoeba histolytica EHI_130980   AAA family ATPase, putative
Entamoeba histolytica EHI_045050   AAA family ATPase, putative
Giardia lamblia GL50803_22138   ATPase, AAA family
Homo sapiens ENSG00000124535   Werner helicase interacting protein 1
Mycobacterium leprae ML0510   Conserved hypothetical protein
Mus musculus ENSMUSG00000021400   Werner helicase interacting protein 1
Mycobacterium tuberculosis Rv2559c   Conserved hypothetical alanine leucine valine rich protein
Mycobacterium ulcerans MUL_1751   recombination factor protein RarA
Neospora caninum NCLIV_066740   ATPase, AAA family domain containing protein, putative
Plasmodium berghei PBANKA_0935000   conserved Plasmodium protein, unknown function
Plasmodium falciparum PF3D7_1112600   DNA helicase, putative
Plasmodium knowlesi PKNH_0910300   conserved Plasmodium protein, unknown function
Plasmodium vivax PVX_091280   hypothetical protein, conserved
Plasmodium yoelii PY05480   putative helicase RUVBL
Saccharomyces cerevisiae YNL218W   ssDNA-dependent ATPase MGS1
Toxoplasma gondii TGME49_251670   werner helicase interacting protein 1, putative

Essentiality

Rv2559c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2603 this record Mycobacterium tuberculosis non-essential nmpdr
b0892 Escherichia coli non-essential goodall
TGME49_251670 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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

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Gene identifier Rv2559c (Mycobacterium tuberculosis), Conserved hypothetical alanine leucine valine rich protein
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