Detailed view for Rv2556c

Basic information

TDR Targets ID: 980929
Mycobacterium tuberculosis, Conserved hypothetical protein

Source Database / ID:  Tuberculist 

pI: 5.4608 | Length (AA): 129 | MW (Da): 13893 | 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

Gene Ontology

Mouse over links to read term descriptions.
No GO information for this protein.

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
2 127 2p6c (A) 8 135 29.00 0 1 1.41424 -0.86
2 127 1vph (A) 8 135 29.00 0 1 1.38864 -0.79
2 127 2p6h (A) 6 132 34.00 0 1 1.41764 -0.83
2 119 2cu5 (A) 7 120 35.00 0.0000003 1 1.26253 -0.31
6 127 1ve0 (A) 13 132 30.00 0 1 1.37164 -0.85

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_128277)

Species Accession Gene Product
Arabidopsis thaliana AT1G21065   hypothetical protein
Candida albicans CaO19.3016   similar to S. pombe hypothetical protein SPAC4A8.02c
Candida albicans CaO19.10534   similar to S. pombe hypothetical protein SPAC4A8.02c
Drosophila melanogaster Dmel_CG31688   CG31688 gene product from transcript CG31688-RD
Escherichia coli b4056   thiamine phosphate synthase
Echinococcus granulosus EgrG_000975400   expressed conserved protein
Entamoeba histolytica EHI_169840   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_000975400   expressed conserved protein
Giardia lamblia GL50803_12942   Hypothetical protein
Mycobacterium tuberculosis Rv2556c   Conserved hypothetical protein
Mycobacterium ulcerans MUL_1753   hypothetical protein
Neospora caninum NCLIV_038300   hypothetical protein, conserved
Oryza sativa 4328549   Os02g0187500
Oryza sativa 4341612   Os06g0638200
Schistosoma japonicum Sjp_0053080   IPR001602,Protein of unknown function UPF0047,domain-containing
Schistosoma japonicum Sjp_0313760   similar to UPF0047 protein C4A8.02c, putative
Schistosoma mansoni Smp_169840   xp-G/rad2 DNA repair endonuclease family member
Schmidtea mediterranea mk4.003279.02   Putative xp-G/rad2 DNA repair endonuclease family member
Toxoplasma gondii TGME49_200470   hypothetical protein
Trichomonas vaginalis TVAG_056840   conserved hypothetical protein
Trichomonas vaginalis TVAG_481010   conserved hypothetical protein

Essentiality

Rv2556c has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b4056 Escherichia coli non-essential goodall
TGME49_200470 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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

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 Rv2556c (Mycobacterium tuberculosis), Conserved hypothetical protein
Title for this comment
Comment