Detailed view for Wbm0707

Basic information

TDR Targets ID: 233107
Wolbachia endosymbiont of Brugia malayi, cold shock protein
Source Database / ID:  GenBank

pI: 8.5042 | Length (AA): 84 | MW (Da): 9601 | 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

PF00313   'Cold-shock' DNA-binding domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0006355   regulation of transcription, DNA-dependent  
GO:0003677   DNA binding  
GO:0003676   nucleic acid binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 3 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
1 82 1c9o (A) 1 66 44.00 0 1 1.36 -1.01
1 62 1c9o (A) 1 51 49.00 0.00000003 0.85 1.15 -0.54
4 70 1mjc (A) 7 61 47.00 0.000000018 1 1.28 -1.34

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_126866)

Species Accession Gene Product
Arabidopsis thaliana AT4G38680   glycine rich protein 2
Arabidopsis thaliana AT2G21060   glycine-rich protein 2B
Brugia malayi Bm1_57515   'Cold-shock' DNA-binding domain containing protein
Caenorhabditis elegans CELE_M01E11.5   Protein CEY-3
Caenorhabditis elegans CELE_F33A8.3   Protein CEY-1
Cryptosporidium hominis Chro.80275   glycogen debranching enzyme
Cryptosporidium parvum cgd8_2340   cold shock RNA binding domain of the OB fold
Drosophila melanogaster Dmel_CG5654   ypsilon schachtel
Escherichia coli b1823   stress protein, member of the CspA-family
Escherichia coli b3556   RNA chaperone and antiterminator, cold-inducible
Escherichia coli b0623   constitutive cold shock family transcription antitermination protein
Escherichia coli b1557   Qin prophage
Escherichia coli b0990   cold shock protein homolog, cold-inducible
Escherichia coli b0880   inhibitor of DNA replication, cold shock protein homolog
Echinococcus multilocularis EmuJ_000490500   nuclease sensitive element binding protein
Homo sapiens ENSG00000065978   Y box binding protein 1
Homo sapiens ENSG00000060138   Y box binding protein 3
Leishmania braziliensis LbrM.28.0880   RNA binding protein rbp16, putative
Leishmania donovani LdBPK_280900.1   RNA binding protein rbp16, putative
Leishmania infantum LinJ.28.0900   RNA binding protein rbp16, putative
Leishmania major LmjF.28.0825   RNA binding protein rbp16, putative
Leishmania mexicana LmxM.28.0825   RNA binding protein rbp16, putative
Loa Loa (eye worm) LOAG_13658   hypothetical protein
Loa Loa (eye worm) LOAG_11791   cold-shock DNA-binding domain-containing protein
Mycobacterium leprae ML0198   Probable cold shock protein A CspA
Mus musculus ENSMUSG00000028639   Y box protein 1
Mus musculus ENSMUSG00000030189   Y box protein 3
Mycobacterium tuberculosis Rv3648c   Probable cold shock protein A CspA
Mycobacterium ulcerans MUL_0392   cold shock protein a, CspA
Mycobacterium ulcerans MUL_0035   DNA-binding protein
Mycobacterium ulcerans MUL_4224   cold-shock protein
Neospora caninum NCLIV_038710   Lin-28 homolog B, related
Neospora caninum NCLIV_009670   Cold-shock protein, DNA-binding, related
Schistosoma japonicum Sjp_0026800   DNA-binding protein A, putative
Schistosoma japonicum Sjp_0200260   ko:K03704 cold shock protein (beta-ribbon, CspA family), putative
Schistosoma mansoni Smp_097800.2   Y box binding protein
Schistosoma mansoni Smp_097750   cold shock domain protein A
Schistosoma mansoni Smp_097800.1   Y box binding protein
Schistosoma mansoni Smp_097800.3   Y box binding protein
Schmidtea mediterranea mk4.003076.00  
Schmidtea mediterranea mk4.009099.00   Y box protein 4-like protein
Schmidtea mediterranea mk4.000460.10   Ypsilon schachtel
Schmidtea mediterranea mk4.001190.00   Ypsilon schachtel
Schmidtea mediterranea mk4.012571.02   Ypsilon schachtel
Schmidtea mediterranea mk4.000038.07  
Schmidtea mediterranea mk4.000460.12   Ypsilon schachtel
Schmidtea mediterranea mk4.023560.00   Ypsilon schachtel
Schmidtea mediterranea mk4.002197.00   Ypsilon schachtel
Schmidtea mediterranea mk4.006230.01  
Schmidtea mediterranea mk4.011408.00  
Schmidtea mediterranea mk4.010663.00  
Schmidtea mediterranea mk4.005229.03  
Schmidtea mediterranea mk4.001230.07   Ypsilon schachtel
Schmidtea mediterranea mk4.001259.05  
Trypanosoma brucei gambiense Tbg972.11.9010   mitochondrial RNA binding protein,RBP16,RNA- binding protein of 16 kDa, putative
Trypanosoma brucei Tb927.11.7900   mitochondrial RNA binding protein 16
Trypanosoma cruzi TcCLB.506933.60   mitochondrial RNA binding protein, putative
Toxoplasma gondii TGME49_320600   cold-shock DNA-binding domain-containing protein
Toxoplasma gondii TGME49_267470   cold-shock DNA-binding domain-containing protein
Theileria parva TP03_0570   cold shock protein, putative
Wolbachia endosymbiont of Brugia malayi Wbm0707   cold shock protein

Essentiality

Wbm0707 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu3710 Mycobacterium tuberculosis essential nmpdr
Tb11.02.5770 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.02.5770 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.02.5770 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.02.5770 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b0623 Escherichia coli non-essential goodall
b0880 Escherichia coli non-essential goodall
b0990 Escherichia coli non-essential goodall
b1557 Escherichia coli non-essential goodall
b1823 Escherichia coli non-essential goodall
b3556 Escherichia coli non-essential goodall
TGME49_267470 Toxoplasma gondii Probably non-essential sidik
TGME49_320600 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • 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

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 Wbm0707 (Wolbachia endosymbiont of Brugia malayi), cold shock protein
Title for this comment
Comment