Rv2871 (vapB43)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: antitoxin
- REFSEQ: hypothetical protein
- PATRIC: FIG00823326: hypothetical protein
- TUBERCULIST: Possible antitoxin VapB43
- NCBI: Possible antitoxin VapB43
- updated information (H37Rv4):
  - gene name: vapB43
  - function:
  - reference:
Type: Not Target
Start: 3183138
End: 3183395
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0045927 - positive regulation of growth (Uniprot)
- GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
Orthologs among selected mycobacteria
Protein structure:
Search for Homologs in PDB
Top 10 Homologs in PDB (as of Nov 2020): (none with >35% aa id)
Links to additional information on vapB43:
- TBDB (updated)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VRTTIRIDDELYREVKAKAARSGRTVAAVLEDAVRRGLNPPKPQAAGRYRVQPSGKGGLRPGVDLSSNAALAEAMNDGVSVDAVR

(Nucleotide sequence available on KEGG)

Additional Information

ESSENTIALITY

MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb

TnSeqCorr - genes with correlated TnSeq profiles across >100 conditions *new*

Classification	Condition	Strain	Method	Reference	Notes
Non-Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 7 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 7 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 7 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000100; 3 non-insertions in a row out of 7 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000050; 3 non-insertions in a row out of 7 sites
Non-Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Non-Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 1.04
Non-Essential	7H09/7H10 + rich media	H37RvMA	MotifHMM	DeJesus et al. (2017)	Fully saturated (14 reps).

TnSeq Data No data currently available.

No TnSeq data currently available for this Target.

RNASeq Data No data currently available.

No RNA-Seq data currently available for this Target.

Metabolomic Profiles No data currently available.

No Metabolomic data currently available for this Target.

Proteomic Data No data currently available.

No Proteomic data currently available for this Target.

Regulatory Relationships from Systems Biology

BioCyc

Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology)

NOTE: Green edges represent the connected genes being classified as differentially essential as a result of the middle gene being knocked out. These interactions are inferred based on RNASeq.

Interactions based on ChIPSeq data

Binds To:
- No bindings to other targets were found.
Bound By:

Interactions based on ChIPSeq data (Minch et al. 2014)

Binds To:
- No bindings to other targets were found.
Bound By:
- No bindings to other targets were found.

Interactions based on TFOE data (Rustad et al. 2014)

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0023 (-)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0238 (-)
- Rv3223c (sigH)

Property	Value	Creator	Evidence	PMID	Comment
Citation	Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: implications for pathogenesis, stress responses, and evolution. authors,HR. Ramage,LE. Connolly,JS. Cox PLoS Genet. 2009	akankshajain.21	IGC	20011113	Gene Neighborhood (Functional linkage)
Interaction	InhibitedBy Rv2872	akankshajain.21	IGC		Gene Neighborhood (Functional linkage) authors,HR. Ramage,LE. Connolly,JS. Cox Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: implications for pathogenesis, stress responses, and evolution. PLoS Genet. 2009
Citation	Solution structure of the Mycobacterium tuberculosis complex protein MPB70: from tuberculosis pathogenesis to inherited human corneal desease. authors,MD. Carr,MJ. Bloemink,E. Dentten,AO. Whelan,SV. Gordon,G. Kelly,TA. Frenkiel,RG. Hewinson,RA. Williamson J. Biol. Chem. 2003	akankshajain.21	IGC	12917404	Gene Neighborhood (Functional linkage)
Interaction	InhibitedBy Rv2872	akankshajain.21	IGC		Gene Neighborhood (Functional linkage) authors,MD. Carr,MJ. Bloemink,E. Dentten,AO. Whelan,SV. Gordon,G. Kelly,TA. Frenkiel,RG. Hewinson,RA. Williamson Solution structure of the Mycobacterium tuberculosis complex protein MPB70: from tuberculosis pathogenesis to inherited human corneal desease. J. Biol. Chem. 2003
Interaction	PhysicalInteraction Rv2872	priti.priety	IEP		Gene Neighborhood (Functional linkage) MD. Jurez, A. Torres et al. Characterization of the Mycobacterium tuberculosis region containing the mpt83 and mpt70 genes. FEMS Microbiol. Lett. 2001

TB Genome Annotation Portal