Rv2547 (vapB19)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: antitoxin
- REFSEQ: hypothetical protein
- PATRIC: DNA-binding protein CopG family
- TUBERCULIST: Possible antitoxin VapB19
- NCBI: Possible antitoxin VapB19
- updated information (H37Rv4):
  - gene name: vapB19
  - function:
  - reference:
Type: Not Target
Start: 2868606
End: 2868863
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)
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 vapB19:
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.621 (from Jeremy Rock's lab)

Amino Acid Sequence

MRTQVTLGKEELELLDRAAKASGASRSELIRRAIHRAYGTGSKQERLAALDHSRGSWRGRDFTGTEYVDAIRGDLNERLARLGLA

(Nucleotide sequence available on KEGG)

Additional Information

Analysis of Positive Selection in Clinical Isolates new

Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
- Moldova: 2,057 clinical isolates
- global set: 5,195 clinical isolates from 15 other countries
In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	NO	NO
omega peak height (95%CI lower bound)	1.03 (0.19)	1.44 (0.46)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link

* example format for variants: "D27 (GAC): D27H (CAC,11)" means "Asp27 (native codon GAC) mutated to His (codon CAC) in 11 isolates"

ESSENTIALITY

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

TnSeqCorr - genes with correlated TnSeq profiles across ~100 conditions

Rv2547/vapB19, gene len: 257 bp, num TA sites: 2

condition	dataset	call	medium	method	notes
in-vitro	DeJesus 2017 mBio	non-essential	7H9	HMM	fully saturated, 14 TnSeq libraries combined
in-vitro	Sassetti 2003 Mol Micro	non-essential	7H9	TRASH	essential if hybridization ratio<0.2
in-vivo (mice)	Sassetti 2003 PNAS	non-essential	BL6 mice	TRASH	essential if hybridization ratio<0.4, min over 4 timepoints (1-8 weeks)
in-vitro (glycerol)	Griffin 2011 PPath	too short	M9 minimal+glycerol	Gumbel	2 replicates; Padj<0.05
in-vitro (cholesterol)	Griffin 2011 PPath	too short	M9 minimal+cholesterol	Gumbel	3 replicates; Padj<0.05
differentially essential in cholesterol	Griffin 2011 PPath	NO (LFC=-0.81)	cholesterol vs glycerol	resampling-SR	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in cholesterol
in-vitro	Smith 2022 eLife	non-essential	7H9	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
in-vivo (mice)	Smith 2022 eLife	non-essential	BL6 mice	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
differentially essential in mice	Smith 2022 eLife	NO (LFC=0.22)	in-vivo vs in-vitro	ZINB	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in mice
in-vitro (minimal)	Minato 2019 mSys	non-essential	minimal medium	HMM
in-vitro (YM rich medium)	Minato 2019 mSys	non-essential	YM rich medium	HMM	7H9 supplemented with ~20 metabolites (amino acids, cofactors)
differentially essential in YM rich medium	Minato 2019 mSys	NO (LFC=1.17)	YM rich vs minimal medium	resampling

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:
- Rv0238 (-)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv3855 (ethR) (Direct binding)
- Rv1049 (-) (Upstream of operon)

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:
- Rv0238 (-)

TBCAP

Tubculosis Community Annotation Project (

Slayden et al., 2013

Rv2547 (vapB19)

Property	Value	Creator	Evidence	PMID	Comment
Citation	The PIN-domain toxin-antitoxin array in mycobacteria. authors,VL. Arcus,PB. Rainey,SJ. Turner Trends Microbiol. 2005	soumisengupta	ISO	15993073	Gene Neighborhood (Functional linkage)
Interaction	Regulatory Rv2548	soumisengupta	ISO		Gene Neighborhood (Functional linkage) authors,VL. Arcus,PB. Rainey,SJ. Turner The PIN-domain toxin-antitoxin array in mycobacteria. Trends Microbiol. 2005
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	soumisengupta	ISO	20011113	Gene Neighborhood (Functional linkage)
Interaction	Regulatory Rv2548	soumisengupta	ISO		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
Interaction	Regulatory Rv2548	soumisengupta	ISO		Gene Neighborhood (Functional linkage) authors,VL. Arcus,PB. Rainey,SJ. Turner The PIN-domain toxin-antitoxin array in mycobacteria. Trends Microbiol. 2005
Interaction	Regulatory Rv2548	soumisengupta	ISO		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
Symbol	VapB	jlew			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	None
Symbol	VapB19	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.
Other	stop:2868863	rslayden			MT1442
Other	strand:+	rslayden			MT1442
Symbol	Vap BC-19	rslayden			MTCY21B4.15c HYPOTHETICAL 9.4 KDA PROTEIN from Mycobacterium tuberculosis (85 aa),FASTA scores: opt: 108, E(): 0.33, (37.1% identity in 62aa overlap); CAC45864
Other	start:2868606	rslayden			MTCY21B4.15c HYPOTHETICAL 9.4 KDA PROTEIN from Mycobacterium tuberculosis (85 aa),FASTA scores: opt: 108, E(): 0.33, (37.1% identity in 62aa overlap); CAC45864
Other	stop:2868863	rslayden			MTCY21B4.15c HYPOTHETICAL 9.4 KDA PROTEIN from Mycobacterium tuberculosis (85 aa),FASTA scores: opt: 108, E(): 0.33, (37.1% identity in 62aa overlap); CAC45864
Other	strand:+	rslayden			MTCY21B4.15c HYPOTHETICAL 9.4 KDA PROTEIN from Mycobacterium tuberculosis (85 aa),FASTA scores: opt: 108, E(): 0.33, (37.1% identity in 62aa overlap); CAC45864
Symbol	Vap BC-19	rslayden			SMC01933 CONSERvED HYPOTHETICAL PROTEIN from Rhizobium meliloti (Sinorhizobium meliloti)(71 aa), FASTA scores: opt: 105, E(): 0.46, (28.4% identity in 74 aa overlap); Q97W38
Other	start:2868606	rslayden			SMC01933 CONSERvED HYPOTHETICAL PROTEIN from Rhizobium meliloti (Sinorhizobium meliloti)(71 aa), FASTA scores: opt: 105, E(): 0.46, (28.4% identity in 74 aa overlap); Q97W38
Other	stop:2868863	rslayden			SMC01933 CONSERvED HYPOTHETICAL PROTEIN from Rhizobium meliloti (Sinorhizobium meliloti)(71 aa), FASTA scores: opt: 105, E(): 0.46, (28.4% identity in 74 aa overlap); Q97W38
Other	strand:+	rslayden			SMC01933 CONSERvED HYPOTHETICAL PROTEIN from Rhizobium meliloti (Sinorhizobium meliloti)(71 aa), FASTA scores: opt: 105, E(): 0.46, (28.4% identity in 74 aa overlap); Q97W38
Symbol	Vap BC-19	rslayden			SSO10342 HYPOTHETICAL PROTEIN from Sulfolobus solfataricus (58 aa), FASTA scores: opt: 94, E(): 2.3, (46.95% identity in 49 aa overlap)
Other	start:2868606	rslayden			SSO10342 HYPOTHETICAL PROTEIN from Sulfolobus solfataricus (58 aa), FASTA scores: opt: 94, E(): 2.3, (46.95% identity in 49 aa overlap)
Other	stop:2868863	rslayden			SSO10342 HYPOTHETICAL PROTEIN from Sulfolobus solfataricus (58 aa), FASTA scores: opt: 94, E(): 2.3, (46.95% identity in 49 aa overlap)
Other	strand:+	rslayden			SSO10342 HYPOTHETICAL PROTEIN from Sulfolobus solfataricus (58 aa), FASTA scores: opt: 94, E(): 2.3, (46.95% identity in 49 aa overlap)
Symbol	Vap BC-19	rslayden			Conserved hypothetical protein. Some similarity to P71666
Other	start:2868606	rslayden			Conserved hypothetical protein. Some similarity to P71666
Other	stop:2868863	rslayden			Conserved hypothetical protein. Some similarity to P71666
Other	strand:+	rslayden			Conserved hypothetical protein. Some similarity to P71666
Symbol	Vap BC-19	rslayden			YD98_MYCTU
Other	start:2868606	rslayden			YD98_MYCTU
Other	stop:2868863	rslayden			YD98_MYCTU
Other	strand:+	rslayden			YD98_MYCTU
Symbol	Vap BC-19	rslayden			Rv1398c
Other	start:2868606	rslayden			Rv1398c
Other	stop:2868863	rslayden			Rv1398c
Other	strand:+	rslayden			Rv1398c
Symbol	Vap BC-19	rslayden			MT1442
Other	start:2868606	rslayden			MT1442

Property

Value

Creator

Evidence

PMID

Comment

Citation

The PIN-domain toxin-antitoxin array in mycobacteria. authors,VL. Arcus,PB. Rainey,SJ. Turner Trends Microbiol. 2005

soumisengupta

ISO

15993073

Gene Neighborhood (Functional linkage)

Interaction

Regulatory Rv2548

soumisengupta

ISO

Gene Neighborhood (Functional linkage)
authors,VL. Arcus,PB. Rainey,SJ. Turner The PIN-domain toxin-antitoxin array in mycobacteria. Trends Microbiol. 2005

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

soumisengupta

ISO

20011113

Gene Neighborhood (Functional linkage)

Interaction

Regulatory Rv2548

soumisengupta

ISO

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

Interaction

Regulatory Rv2548

soumisengupta

ISO

Gene Neighborhood (Functional linkage)
authors,VL. Arcus,PB. Rainey,SJ. Turner The PIN-domain toxin-antitoxin array in mycobacteria. Trends Microbiol. 2005

Interaction

Regulatory Rv2548

soumisengupta

ISO

Symbol

VapB

jlew

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

None

Symbol

VapB19

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

Other

stop:2868863

rslayden

MT1442

Other

strand:+

rslayden

MT1442

Symbol

Vap BC-19

rslayden

MTCY21B4.15c HYPOTHETICAL 9.4 KDA PROTEIN from Mycobacterium tuberculosis (85 aa),FASTA scores: opt: 108, E(): 0.33, (37.1% identity in 62aa overlap); CAC45864

Other

start:2868606

rslayden

MTCY21B4.15c HYPOTHETICAL 9.4 KDA PROTEIN from Mycobacterium tuberculosis (85 aa),FASTA scores: opt: 108, E(): 0.33, (37.1% identity in 62aa overlap); CAC45864

Other

stop:2868863

rslayden

MTCY21B4.15c HYPOTHETICAL 9.4 KDA PROTEIN from Mycobacterium tuberculosis (85 aa),FASTA scores: opt: 108, E(): 0.33, (37.1% identity in 62aa overlap); CAC45864

Other

strand:+

rslayden

MTCY21B4.15c HYPOTHETICAL 9.4 KDA PROTEIN from Mycobacterium tuberculosis (85 aa),FASTA scores: opt: 108, E(): 0.33, (37.1% identity in 62aa overlap); CAC45864

Symbol

Vap BC-19

rslayden

SMC01933 CONSERvED HYPOTHETICAL PROTEIN from Rhizobium meliloti (Sinorhizobium meliloti)(71 aa), FASTA scores: opt: 105, E(): 0.46, (28.4% identity in 74 aa overlap); Q97W38

Other

start:2868606

rslayden

SMC01933 CONSERvED HYPOTHETICAL PROTEIN from Rhizobium meliloti (Sinorhizobium meliloti)(71 aa), FASTA scores: opt: 105, E(): 0.46, (28.4% identity in 74 aa overlap); Q97W38

Other

stop:2868863

rslayden

SMC01933 CONSERvED HYPOTHETICAL PROTEIN from Rhizobium meliloti (Sinorhizobium meliloti)(71 aa), FASTA scores: opt: 105, E(): 0.46, (28.4% identity in 74 aa overlap); Q97W38

Other

strand:+

rslayden

SMC01933 CONSERvED HYPOTHETICAL PROTEIN from Rhizobium meliloti (Sinorhizobium meliloti)(71 aa), FASTA scores: opt: 105, E(): 0.46, (28.4% identity in 74 aa overlap); Q97W38

Symbol

Vap BC-19

rslayden

SSO10342 HYPOTHETICAL PROTEIN from Sulfolobus solfataricus (58 aa), FASTA scores: opt: 94, E(): 2.3, (46.95% identity in 49 aa overlap)

Other

start:2868606

rslayden

SSO10342 HYPOTHETICAL PROTEIN from Sulfolobus solfataricus (58 aa), FASTA scores: opt: 94, E(): 2.3, (46.95% identity in 49 aa overlap)

Other

stop:2868863

rslayden

SSO10342 HYPOTHETICAL PROTEIN from Sulfolobus solfataricus (58 aa), FASTA scores: opt: 94, E(): 2.3, (46.95% identity in 49 aa overlap)

Other

strand:+

rslayden

SSO10342 HYPOTHETICAL PROTEIN from Sulfolobus solfataricus (58 aa), FASTA scores: opt: 94, E(): 2.3, (46.95% identity in 49 aa overlap)

Symbol

Vap BC-19

rslayden

Conserved hypothetical protein. Some similarity to P71666

Other

start:2868606

rslayden

Conserved hypothetical protein. Some similarity to P71666

Other

stop:2868863

rslayden

Conserved hypothetical protein. Some similarity to P71666

Other

strand:+

rslayden

Conserved hypothetical protein. Some similarity to P71666

Symbol

Vap BC-19

rslayden

YD98_MYCTU

Other

start:2868606

rslayden

YD98_MYCTU

Other

stop:2868863

rslayden

YD98_MYCTU

Other

strand:+

rslayden

YD98_MYCTU

Symbol

Vap BC-19

rslayden

Rv1398c

Other

start:2868606

rslayden

Rv1398c

Other

stop:2868863

rslayden

Rv1398c

Other

strand:+

rslayden

Rv1398c

Symbol

Vap BC-19

rslayden

MT1442

Other

start:2868606

rslayden

MT1442

Comments

TB Genome Annotation Portal

Rv2547 (vapB19)

Amino Acid Sequence

Additional Information

Analysis of Positive Selection in Clinical Isolates *new*

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

Interactions based on ChIPSeq data

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

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

TBCAP

Comments

Analysis of Positive Selection in Clinical Isolates new