Rv2830c (vapB22)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: antitoxin
- REFSEQ: hypothetical protein
- PATRIC: FIG00821747: hypothetical protein
- TUBERCULIST: Possible antitoxin VapB22
- NCBI: Possible antitoxin VapB22
- updated information (H37Rv4):
  - gene name: vapB22
  - function:
  - reference:
Type: Not Target
Start: 3137009
End: 3137224
Operon:

Trans-membrane region:
Role: IV.B.3 - Phage-related functions
GO terms:
- GO:0045727 - positive regulation of translation (Uniprot)
- GO:0040007 - growth (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 vapB22:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 1.036 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MTATEVKAKILSLLDEVAQGEEIEITKHGRTVARLVAATGPHALKGRFSGVAMAAADDDELFTTGVSWNVS

(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
Too-Short	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 1 sites
Too-Short	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 1 sites
Too-Short	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 1 sites
Too-Short	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 1 sites
Too-Short	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 1 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.09
Uncertain	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:
- Not upregulated by other genes.
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0019c (fhaB)
- Rv0047c (-)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	RegulatedBy Rv3133c	yamir.moreno	IEP		Microarrays. mRNA levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using microarray (or macroarray) experiments.. HD. Park, KM. Guinn et al. Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis. Mol. Microbiol. 2003
Symbol	VapB	jlew			Rescues growth inhibition in MS authors,BA. Ahidjo,D. Kuhnert,JL. McKenzie,EE. Machowski,BG. Gordhan,V. Arcus,GL. Abrahams,V. Mizrahi VapC toxins from Mycobacterium tuberculosis are ribonucleases that differentially inhibit growth and are neutralized by cognate VapB antitoxins. PLoS ONE 2011
Citation	VapC toxins from Mycobacterium tuberculosis are ribonucleases that differentially inhibit growth and are neutralized by cognate VapB antitoxins. authors,BA. Ahidjo,D. Kuhnert,JL. McKenzie,EE. Machowski,BG. Gordhan,V. Arcus,GL. Abrahams,V. Mizrahi PLoS ONE 2011	jlew		21738782	Rescues growth inhibition in MS
Symbol	VapB22	jlew			We report the heterologous toxicity of these TA loci in Escherichia coli and show that only a few of the M. tuberculosis-encoded toxins can inhibit E. coli growth and have a killing effect. This killing effect can be suppressed by coexpression of the cognate antitoxin. authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009
Citation	Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. authors,A. Gupta FEMS Microbiol. Lett. 2009	jlew		19016878	We report the heterologous toxicity of these TA loci in Escherichia coli and show that only a few of the M. tuberculosis-encoded toxins can inhibit E. coli growth and have a killing effect. This killing effect can be suppressed by coexpression of the cognate antitoxin.
Symbol	Vap BC-22	rslayden			Hypothetical protein, some similarity to Z97182
Other	start:3137009	rslayden			Hypothetical protein, some similarity to Z97182
Other	stop:3137224	rslayden			Hypothetical protein, some similarity to Z97182
Other	strand:+	rslayden			Hypothetical protein, some similarity to Z97182
Symbol	Vap BC-22	rslayden			MTCY19H5.26
Other	start:3137009	rslayden			MTCY19H5.26
Other	stop:3137224	rslayden			MTCY19H5.26
Other	strand:+	rslayden			MTCY19H5.26
Symbol	Vap BC-22	rslayden			Rv0596c Hypothetical protein from Mycobacterium tuberculosis (85aa), FASTA scores: opt: 88, E(): 1.3, (41.7% identity in 36 aa overlap); and to PHD_BPP1
Other	start:3137009	rslayden			Rv0596c Hypothetical protein from Mycobacterium tuberculosis (85aa), FASTA scores: opt: 88, E(): 1.3, (41.7% identity in 36 aa overlap); and to PHD_BPP1
Other	stop:3137224	rslayden			Rv0596c Hypothetical protein from Mycobacterium tuberculosis (85aa), FASTA scores: opt: 88, E(): 1.3, (41.7% identity in 36 aa overlap); and to PHD_BPP1
Other	strand:+	rslayden			Rv0596c Hypothetical protein from Mycobacterium tuberculosis (85aa), FASTA scores: opt: 88, E(): 1.3, (41.7% identity in 36 aa overlap); and to PHD_BPP1
Symbol	Vap BC-22	rslayden			Q06253 bacteriophage P1 phd gene (73 aa), FASTA scores: opt: 79, E(): 3.8, (35.9% identity in 39 aa overlap)
Other	start:3137009	rslayden			Q06253 bacteriophage P1 phd gene (73 aa), FASTA scores: opt: 79, E(): 3.8, (35.9% identity in 39 aa overlap)
Other	stop:3137224	rslayden			Q06253 bacteriophage P1 phd gene (73 aa), FASTA scores: opt: 79, E(): 3.8, (35.9% identity in 39 aa overlap)
Other	strand:+	rslayden			Q06253 bacteriophage P1 phd gene (73 aa), FASTA scores: opt: 79, E(): 3.8, (35.9% identity in 39 aa overlap)

TB Genome Annotation Portal