Rv1560 (vapB11)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: antitoxin
- REFSEQ: hypothetical protein
- PATRIC: FIG00821924: hypothetical protein
- TUBERCULIST: Possible antitoxin VapB11
- NCBI: Possible antitoxin VapB11
- updated information (H37Rv4):
  - gene name: vapB11
  - function:
  - reference:
Type: Conditional
Start: 1764755
End: 1764973
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0075136 - response to host (Uniprot)
- GO:0045927 - positive regulation of growth (Uniprot)
- GO:0045727 - positive regulation of translation (Uniprot)
- GO:0005515 - protein binding (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):

PDB	aa ident	species	PDB title
6A7V	100%	Mycobacterium tuberculosis H37Rv	Crystal structure of Mycobacterium tuberculosis VapBC11 toxin-antitoxin complex
4CHG	52%	MYCOBACTERIUM TUBERCULOSIS	Crystal structure of VapBC15 complex from Mycobacterium tuberculosis

Links to additional information on vapB11:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.107 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VYRWCMSRTNIDIDDELAAEVMRRFGLTTKRAAVDLALRRLVGSPLSREFLLGLEGVGWEGDLDDLRSDRPD

(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 3 sites
Too-Short	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 3 sites
Too-Short	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 0 non-insertions in a row out of 3 sites
Too-Short	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: -1.000000; 2 non-insertions in a row out of 3 sites
Too-Short	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: -1.000000; 3 non-insertions in a row out of 3 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: 0.41
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:
Bound By:
- Rv0238 (-)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0047c (-) (Direct binding)
- Rv2250c (-) (Direct binding)
- Rv0135c (-) (Upstream of operon)
- Rv1353c (-) (Upstream of operon)
- Rv1556 (-) (Upstream of operon)

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

Upregulates:
- Rv1560 (vapB11)
- Rv1561 (vapC11)
Upregulated by:
- Rv1560 (vapB11)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0238 (-)

Property	Value	Creator	Evidence	PMID	Comment
Citation	Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. authors,A. Gupta FEMS Microbiol. Lett. 2009	vizhi.gurusamy	NAS	19016878	Functional linkage (Gene neighborhood)
Interaction	Inhibits Rv1561	vizhi.gurusamy	NAS		Functional linkage (Gene neighborhood) authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009
Interaction	InhibitedBy Rv1561	vizhi.gurusamy	NAS		Functional linkage (Gene neighborhood) authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009
Interaction	InhibitedBy Rv1561	vizhi.gurusamy	NAS		Functional linkage (Gene neighborhood) 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	VapB11	jlew			Relieves toxin activity. 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	Relieves toxin activity. 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	strand:+	rslayden			Rv2009
Symbol	Vap BC-11	rslayden			MTCY39.08c (80 aa), FASTA score: (54.4% identity in 68 aa overlap); Q10799
Other	start:1764755	rslayden			MTCY39.08c (80 aa), FASTA score: (54.4% identity in 68 aa overlap); Q10799
Other	stop:1764973	rslayden			MTCY39.08c (80 aa), FASTA score: (54.4% identity in 68 aa overlap); Q10799
Other	strand:+	rslayden			MTCY39.08c (80 aa), FASTA score: (54.4% identity in 68 aa overlap); Q10799
Symbol	Vap BC-11	rslayden			Rv2871
Other	start:1764755	rslayden			Rv2871
Other	stop:1764973	rslayden			Rv2871
Other	strand:+	rslayden			Rv2871
Symbol	Vap BC-11	rslayden			MTCY274.02 (85 aa); O50456
Other	start:1764755	rslayden			MTCY274.02 (85 aa); O50456
Other	stop:1764973	rslayden			MTCY274.02 (85 aa); O50456
Other	strand:+	rslayden			MTCY274.02 (85 aa); O50456
Symbol	Vap BC-11	rslayden			Rv1241
Other	start:1764755	rslayden			Rv1241
Other	stop:1764973	rslayden			Rv1241
Other	strand:+	rslayden			Rv1241
Symbol	Vap BC-11	rslayden			MTV006.13 (86 aa), O06243
Other	start:1764755	rslayden			MTV006.13 (86 aa), O06243
Other	stop:1764973	rslayden			MTV006.13 (86 aa), O06243
Other	strand:+	rslayden			MTV006.13 (86 aa), O06243
Symbol	Vap BC-11	rslayden			Rv2132
Other	start:1764755	rslayden			Rv2132
Other	stop:1764973	rslayden			Rv2132
Other	strand:+	rslayden			Rv2132
Symbol	Vap BC-11	rslayden			MTCY270.36C (76 aa); etc.
Other	start:1764755	rslayden			MTCY270.36C (76 aa); etc.
Other	stop:1764973	rslayden			MTCY270.36C (76 aa); etc.
Other	strand:+	rslayden			MTCY270.36C (76 aa); etc.
Symbol	Vap BC-11	rslayden			Conserved hypothetical protein, part of a Mycobacterial tuberculosis family of proteins e.g. Q10848
Other	start:1764755	rslayden			Conserved hypothetical protein, part of a Mycobacterial tuberculosis family of proteins e.g. Q10848
Other	stop:1764973	rslayden			Conserved hypothetical protein, part of a Mycobacterial tuberculosis family of proteins e.g. Q10848
Other	strand:+	rslayden			Conserved hypothetical protein, part of a Mycobacterial tuberculosis family of proteins e.g. Q10848
Symbol	Vap BC-11	rslayden			Rv2009
Other	start:1764755	rslayden			Rv2009
Other	stop:1764973	rslayden			Rv2009

TB Genome Annotation Portal