Rv2545 (vapB18)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: antitoxin
- REFSEQ: hypothetical protein
- PATRIC: hypothetical protein Rv2545
- TUBERCULIST: Possible antitoxin VapB18
- NCBI: Possible antitoxin VapB18
- updated information (H37Rv4):
  - gene name: vapB18
  - function:
  - reference:
Type: Not Target
Start: 2867783
End: 2868061
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- No terms assigned.
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 vapB18:
- 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 = 0.974 (from Jeremy Rock's lab)

Amino Acid Sequence

VSTTIVAGVIQGHLPVILPTRRRARDLGHTTALFRAQTLQCIYLSIEYLYVCSMSRRTTIDIDDILLARAQAALGTTGLKDRVDAALRAAVR

(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 10 sites
Too-Short	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 10 sites
Too-Short	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 10 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 11 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 11 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: 3.89
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:
- Rv0465c (-) (Direct binding)
- Rv2887 (-) (Upstream of operon)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0022c (whiB5)
- Rv0818 (-)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0023 (-)

TBCAP

Tubculosis Community Annotation Project (

Slayden et al., 2013

Rv2545 (vapB18)

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 Rv2546	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 Rv2546	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 Rv2546	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 Rv2546	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	VapB18	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-18	rslayden			MTV002.23c PROTEIN from Mycobacterium tuberculosis (88 aa), FASTA scores: opt: 151, E():9.8e-05, (66.65% identity in 45 aa overlap); and Q10771
Other	start:2867783	rslayden			MTV002.23c PROTEIN from Mycobacterium tuberculosis (88 aa), FASTA scores: opt: 151, E():9.8e-05, (66.65% identity in 45 aa overlap); and Q10771
Other	stop:2868061	rslayden			MTV002.23c PROTEIN from Mycobacterium tuberculosis (88 aa), FASTA scores: opt: 151, E():9.8e-05, (66.65% identity in 45 aa overlap); and Q10771
Other	strand:+	rslayden			MTV002.23c PROTEIN from Mycobacterium tuberculosis (88 aa), FASTA scores: opt: 151, E():9.8e-05, (66.65% identity in 45 aa overlap); and Q10771
Symbol	Vap BC-18	rslayden			Rv1560
Other	start:2867783	rslayden			Rv1560
Other	stop:2868061	rslayden			Rv1560
Other	strand:+	rslayden			Rv1560
Symbol	Vap BC-18	rslayden			MT1611
Other	start:2867783	rslayden			MT1611
Other	stop:2868061	rslayden			MT1611
Other	strand:+	rslayden			MT1611
Symbol	Vap BC-18	rslayden			MTCY48.05 PROTEIN from Mycobacterium tuberculosis (72 aa), FASTA scores: opt: 84, E(): 8.2,(46.5% identity in 43 aa overlap)
Other	start:2867783	rslayden			MTCY48.05 PROTEIN from Mycobacterium tuberculosis (72 aa), FASTA scores: opt: 84, E(): 8.2,(46.5% identity in 43 aa overlap)
Other	stop:2868061	rslayden			MTCY48.05 PROTEIN from Mycobacterium tuberculosis (72 aa), FASTA scores: opt: 84, E(): 8.2,(46.5% identity in 43 aa overlap)
Other	strand:+	rslayden			MTCY48.05 PROTEIN from Mycobacterium tuberculosis (72 aa), FASTA scores: opt: 84, E(): 8.2,(46.5% identity in 43 aa overlap)
Symbol	Vap BC-18	rslayden			Conserved hypothetical protein. C-terminus highly similar to O33300
Other	start:2867783	rslayden			Conserved hypothetical protein. C-terminus highly similar to O33300
Other	stop:2868061	rslayden			Conserved hypothetical protein. C-terminus highly similar to O33300
Other	strand:+	rslayden			Conserved hypothetical protein. C-terminus highly similar to O33300
Symbol	Vap BC-18	rslayden			Rv2758c
Other	start:2867783	rslayden			Rv2758c
Other	stop:2868061	rslayden			Rv2758c
Other	strand:+	rslayden			Rv2758c

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 Rv2546

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 Rv2546

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 Rv2546

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 Rv2546

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

VapB18

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

Symbol

Vap BC-18

rslayden

MTV002.23c PROTEIN from Mycobacterium tuberculosis (88 aa), FASTA scores: opt: 151, E():9.8e-05, (66.65% identity in 45 aa overlap); and Q10771

Other

start:2867783

rslayden

MTV002.23c PROTEIN from Mycobacterium tuberculosis (88 aa), FASTA scores: opt: 151, E():9.8e-05, (66.65% identity in 45 aa overlap); and Q10771

Other

stop:2868061

rslayden

MTV002.23c PROTEIN from Mycobacterium tuberculosis (88 aa), FASTA scores: opt: 151, E():9.8e-05, (66.65% identity in 45 aa overlap); and Q10771

Other

strand:+

rslayden

MTV002.23c PROTEIN from Mycobacterium tuberculosis (88 aa), FASTA scores: opt: 151, E():9.8e-05, (66.65% identity in 45 aa overlap); and Q10771

Symbol

Vap BC-18

rslayden

Rv1560

Other

start:2867783

rslayden

Rv1560

Other

stop:2868061

rslayden

Rv1560

Other

strand:+

rslayden

Rv1560

Symbol

Vap BC-18

rslayden

MT1611

Other

start:2867783

rslayden

MT1611

Other

stop:2868061

rslayden

MT1611

Other

strand:+

rslayden

MT1611

Symbol

Vap BC-18

rslayden

MTCY48.05 PROTEIN from Mycobacterium tuberculosis (72 aa), FASTA scores: opt: 84, E(): 8.2,(46.5% identity in 43 aa overlap)

Other

start:2867783

rslayden

MTCY48.05 PROTEIN from Mycobacterium tuberculosis (72 aa), FASTA scores: opt: 84, E(): 8.2,(46.5% identity in 43 aa overlap)

Other

stop:2868061

rslayden

MTCY48.05 PROTEIN from Mycobacterium tuberculosis (72 aa), FASTA scores: opt: 84, E(): 8.2,(46.5% identity in 43 aa overlap)

Other

strand:+

rslayden

MTCY48.05 PROTEIN from Mycobacterium tuberculosis (72 aa), FASTA scores: opt: 84, E(): 8.2,(46.5% identity in 43 aa overlap)

Symbol

Vap BC-18

rslayden

Conserved hypothetical protein. C-terminus highly similar to O33300

Other

start:2867783

rslayden

Conserved hypothetical protein. C-terminus highly similar to O33300

Other

stop:2868061

rslayden

Conserved hypothetical protein. C-terminus highly similar to O33300

Other

strand:+

rslayden

Conserved hypothetical protein. C-terminus highly similar to O33300

Symbol

Vap BC-18

rslayden

Rv2758c

Other

start:2867783

rslayden

Rv2758c

Other

stop:2868061

rslayden

Rv2758c

Other

strand:+

rslayden

Rv2758c

Comments