Rv0657c (vapB6)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: antitoxin
- REFSEQ: hypothetical protein
- PATRIC: FIG00821248: hypothetical protein
- TUBERCULIST: Possible antitoxin VapB6
- NCBI: Possible antitoxin VapB6
- updated information (H37Rv4):
  - gene name: vapB6
  - function:
  - reference:
Type: Not Target
Start: 753462
End: 753617
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 vapB6:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = ? (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VSVTQIDLDDEALADVMRIAAVHTKKEAVNLAMRDYVERFRRIEALARSRE

(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; 0 non-insertions in a row out of 1 sites
Too-Short	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 0 non-insertions in a row out of 1 sites
Too-Short	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 0 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 2 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 2 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: 3.38
Growth-Advantage	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:
- Rv0023 (-) (Direct binding)
- Rv0047c (-) (Direct binding)
- Rv0081 (-) (Direct binding)
- Rv1033c (trcR) (Direct binding)

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:

TBCAP

Tubculosis Community Annotation Project (

Slayden et al., 2013

Rv0657c (vapB6)

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	ashwinigbhat	IGC	20011113	Gene Neighborhood (Functional linkage)
Interaction	Inhibits Rv0656c	ashwinigbhat	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
Interaction	Inhibits Rv0656c	priti.priety	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
Interaction	Inhibits Rv0656c	ashwinigbhat	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	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	priti.priety	IGC	20011113	Gene Neighborhood (Functional linkage)
Interaction	Inhibits Rv0656c	priti.priety	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
Symbol	VapB6	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:753617	rslayden			MTCY39.08c
Other	strand:+	rslayden			MTCY39.08c
Symbol	Vap BC-6	rslayden			YW08_MYCTU
Other	start:753462	rslayden			YW08_MYCTU
Other	stop:753617	rslayden			YW08_MYCTU
Other	strand:+	rslayden			YW08_MYCTU
Symbol	Vap BC-6	rslayden			Q10848 (80 aa),FASTA scores: opt: 107, E(): 0.0038, (45.8% identity in 48 aa overlap), Rv2871, Rv1560, etc. Also some similarity with AL020958
Other	start:753462	rslayden			Q10848 (80 aa),FASTA scores: opt: 107, E(): 0.0038, (45.8% identity in 48 aa overlap), Rv2871, Rv1560, etc. Also some similarity with AL020958
Other	stop:753617	rslayden			Q10848 (80 aa),FASTA scores: opt: 107, E(): 0.0038, (45.8% identity in 48 aa overlap), Rv2871, Rv1560, etc. Also some similarity with AL020958
Other	strand:+	rslayden			Q10848 (80 aa),FASTA scores: opt: 107, E(): 0.0038, (45.8% identity in 48 aa overlap), Rv2871, Rv1560, etc. Also some similarity with AL020958
Symbol	Vap BC-6	rslayden			SC4H8_7 from Streptomyces coelicolor (66aa), FASTA score: (41.0% identity in 39 aa overlap)
Other	start:753462	rslayden			SC4H8_7 from Streptomyces coelicolor (66aa), FASTA score: (41.0% identity in 39 aa overlap)
Other	stop:753617	rslayden			SC4H8_7 from Streptomyces coelicolor (66aa), FASTA score: (41.0% identity in 39 aa overlap)
Other	strand:+	rslayden			SC4H8_7 from Streptomyces coelicolor (66aa), FASTA score: (41.0% identity in 39 aa overlap)
Other	start:753462	rslayden			MTCY39.08c
Symbol	Vap BC-6	rslayden			Conserved hypothetical protein, showing similarity with hypothetical proteins from Mycobacterium tuberculosis e.g. Rv2009
Other	start:753462	rslayden			Conserved hypothetical protein, showing similarity with hypothetical proteins from Mycobacterium tuberculosis e.g. Rv2009
Other	stop:753617	rslayden			Conserved hypothetical protein, showing similarity with hypothetical proteins from Mycobacterium tuberculosis e.g. Rv2009
Other	strand:+	rslayden			Conserved hypothetical protein, showing similarity with hypothetical proteins from Mycobacterium tuberculosis e.g. Rv2009
Symbol	Vap BC-6	rslayden			MT2064.1
Other	start:753462	rslayden			MT2064.1
Other	stop:753617	rslayden			MT2064.1
Other	strand:+	rslayden			MT2064.1
Symbol	Vap BC-6	rslayden			MTCY39.08c

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

ashwinigbhat

IGC

20011113

Gene Neighborhood (Functional linkage)

Interaction

Inhibits Rv0656c

ashwinigbhat

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

Interaction

Inhibits Rv0656c

priti.priety

IGC

Interaction

Inhibits Rv0656c

ashwinigbhat

IGC

Citation

priti.priety

IGC

20011113

Gene Neighborhood (Functional linkage)

Interaction

Inhibits Rv0656c

priti.priety

IGC

Symbol

VapB6

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:753617

rslayden

MTCY39.08c

Other

strand:+

rslayden

MTCY39.08c

Symbol

Vap BC-6

rslayden

YW08_MYCTU

Other

start:753462

rslayden

YW08_MYCTU

Other

stop:753617

rslayden

YW08_MYCTU

Other

strand:+

rslayden

YW08_MYCTU

Symbol

Vap BC-6

rslayden

Q10848 (80 aa),FASTA scores: opt: 107, E(): 0.0038, (45.8% identity in 48 aa overlap), Rv2871, Rv1560, etc. Also some similarity with AL020958

Other

start:753462

rslayden

Q10848 (80 aa),FASTA scores: opt: 107, E(): 0.0038, (45.8% identity in 48 aa overlap), Rv2871, Rv1560, etc. Also some similarity with AL020958

Other

stop:753617

rslayden

Q10848 (80 aa),FASTA scores: opt: 107, E(): 0.0038, (45.8% identity in 48 aa overlap), Rv2871, Rv1560, etc. Also some similarity with AL020958

Other

strand:+

rslayden

Q10848 (80 aa),FASTA scores: opt: 107, E(): 0.0038, (45.8% identity in 48 aa overlap), Rv2871, Rv1560, etc. Also some similarity with AL020958

Symbol

Vap BC-6

rslayden

SC4H8_7 from Streptomyces coelicolor (66aa), FASTA score: (41.0% identity in 39 aa overlap)

Other

start:753462

rslayden

SC4H8_7 from Streptomyces coelicolor (66aa), FASTA score: (41.0% identity in 39 aa overlap)

Other

stop:753617

rslayden

SC4H8_7 from Streptomyces coelicolor (66aa), FASTA score: (41.0% identity in 39 aa overlap)

Other

strand:+

rslayden

SC4H8_7 from Streptomyces coelicolor (66aa), FASTA score: (41.0% identity in 39 aa overlap)

Other

start:753462

rslayden

MTCY39.08c

Symbol

Vap BC-6

rslayden

Conserved hypothetical protein, showing similarity with hypothetical proteins from Mycobacterium tuberculosis e.g. Rv2009

Other

start:753462

rslayden

Conserved hypothetical protein, showing similarity with hypothetical proteins from Mycobacterium tuberculosis e.g. Rv2009

Other

stop:753617

rslayden

Conserved hypothetical protein, showing similarity with hypothetical proteins from Mycobacterium tuberculosis e.g. Rv2009

Other

strand:+

rslayden

Conserved hypothetical protein, showing similarity with hypothetical proteins from Mycobacterium tuberculosis e.g. Rv2009

Symbol

Vap BC-6

rslayden

MT2064.1

Other

start:753462

rslayden

MT2064.1

Other

stop:753617

rslayden

MT2064.1

Other

strand:+

rslayden

MT2064.1

Symbol

Vap BC-6

rslayden

MTCY39.08c

Comments