Rv2758c (vapB21)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: antitoxin
- REFSEQ: hypothetical protein
- PATRIC: FIG00821100: hypothetical protein
- TUBERCULIST: Possible antitoxin VapB21
- NCBI: Possible antitoxin VapB21
- updated information (H37Rv4):
  - gene name: vapB21
  - function:
  - reference:
Type: Conditional
Start: 3070583
End: 3070849
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0045927 - positive regulation of 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 vapB21:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.084 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MHRGYALVVCSPGVTRTMIDIDDDLLARAAKELGTTTKKDTVHAALRAALRASAARSLMNRMAENATGTQDEALVNAMWRDGHPENTA

(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 5 sites
Too-Short	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 5 sites
Too-Short	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 5 sites
Too-Short	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: -1.000000; 3 non-insertions in a row out of 5 sites
Too-Short	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: -1.000000; 2 non-insertions in a row out of 5 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: 3.24
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:
- Rv0047c (-) (Direct binding)
- Rv3246c (mtrA) (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

Rv2758c (vapB21)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Inhibits Rv2757c	vizhi.gurusamy	IEP		Co-expression (Functional linkage) authors,VL. Arcus,PB. Rainey,SJ. Turner The PIN-domain toxin-antitoxin array in mycobacteria. Trends Microbiol. 2005
Interaction	Inhibits Rv2757c	vizhi.gurusamy	IEP		Co-expression (Functional linkage) authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009
Citation	Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. authors,DP. Pandey,K. Gerdes Nucleic Acids Res. 2005	vizhi.gurusamy	IEP	15718296	Co-expression (Functional linkage)
Interaction	Inhibits Rv2757c	vizhi.gurusamy	IEP		Co-expression (Functional linkage) authors,DP. Pandey,K. Gerdes Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res. 2005
Citation	The PIN-domain toxin-antitoxin array in mycobacteria. authors,VL. Arcus,PB. Rainey,SJ. Turner Trends Microbiol. 2005	vizhi.gurusamy	IEP	15993073	Co-expression (Functional linkage)
Interaction	Inhibits Rv2757c	vizhi.gurusamy	IEP		Co-expression (Functional linkage) authors,VL. Arcus,PB. Rainey,SJ. Turner The PIN-domain toxin-antitoxin array in mycobacteria. Trends Microbiol. 2005
Symbol	VapB21	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:3070849	rslayden			MTCY48.05c (72 aa), FASTA scores: opt: 106, E(): 0.52, (39.15% identity in 46 aa overlap); O06565
Other	strand:+	rslayden			MTCY48.05c (72 aa), FASTA scores: opt: 106, E(): 0.52, (39.15% identity in 46 aa overlap); O06565
Symbol	Vap BC-21	rslayden			Rv1113
Other	start:3070583	rslayden			Rv1113
Other	stop:3070849	rslayden			Rv1113
Other	strand:+	rslayden			Rv1113
Symbol	Vap BC-21	rslayden			MTCY22G8.02 (65 aa), FASTA scores: opt: 97, E(): 2.2, (33.35% identity in 69 aa overlap); etc. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp signature.
Other	start:3070583	rslayden			MTCY22G8.02 (65 aa), FASTA scores: opt: 97, E(): 2.2, (33.35% identity in 69 aa overlap); etc. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp signature.
Other	stop:3070849	rslayden			MTCY22G8.02 (65 aa), FASTA scores: opt: 97, E(): 2.2, (33.35% identity in 69 aa overlap); etc. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp signature.
Other	strand:+	rslayden			MTCY22G8.02 (65 aa), FASTA scores: opt: 97, E(): 2.2, (33.35% identity in 69 aa overlap); etc. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp signature.
Symbol	Vap BC-21	rslayden			Conserved hypothetical protein, similar to several other M. tuberculosis hypothetical proteins e.g. P95008
Other	start:3070583	rslayden			Conserved hypothetical protein, similar to several other M. tuberculosis hypothetical proteins e.g. P95008
Other	stop:3070849	rslayden			Conserved hypothetical protein, similar to several other M. tuberculosis hypothetical proteins e.g. P95008
Other	strand:+	rslayden			Conserved hypothetical protein, similar to several other M. tuberculosis hypothetical proteins e.g. P95008
Symbol	Vap BC-21	rslayden			Rv2545 (92 aa), FASTA scores: opt: 151, E(): 0.00028, (66.65%identity in 45 aa overlap); Q10771
Other	start:3070583	rslayden			Rv2545 (92 aa), FASTA scores: opt: 151, E(): 0.00028, (66.65%identity in 45 aa overlap); Q10771
Other	stop:3070849	rslayden			Rv2545 (92 aa), FASTA scores: opt: 151, E(): 0.00028, (66.65%identity in 45 aa overlap); Q10771
Other	strand:+	rslayden			Rv2545 (92 aa), FASTA scores: opt: 151, E(): 0.00028, (66.65%identity in 45 aa overlap); Q10771
Symbol	Vap BC-21	rslayden			YF60_MYCTU
Other	start:3070583	rslayden			YF60_MYCTU
Other	stop:3070849	rslayden			YF60_MYCTU
Other	strand:+	rslayden			YF60_MYCTU
Symbol	Vap BC-21	rslayden			Rv1560
Other	start:3070583	rslayden			Rv1560
Other	stop:3070849	rslayden			Rv1560
Other	strand:+	rslayden			Rv1560
Symbol	Vap BC-21	rslayden			MT1611
Other	start:3070583	rslayden			MT1611
Other	stop:3070849	rslayden			MT1611
Other	strand:+	rslayden			MT1611
Symbol	Vap BC-21	rslayden			MTCY48.05c (72 aa), FASTA scores: opt: 106, E(): 0.52, (39.15% identity in 46 aa overlap); O06565
Other	start:3070583	rslayden			MTCY48.05c (72 aa), FASTA scores: opt: 106, E(): 0.52, (39.15% identity in 46 aa overlap); O06565

Property

Value

Creator

Evidence

PMID

Comment

Interaction

Inhibits Rv2757c

vizhi.gurusamy

IEP

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

Interaction

Inhibits Rv2757c

vizhi.gurusamy

IEP

Co-expression (Functional linkage)
authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009

Citation

Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. authors,DP. Pandey,K. Gerdes Nucleic Acids Res. 2005

vizhi.gurusamy

IEP

15718296

Co-expression (Functional linkage)

Interaction

Inhibits Rv2757c

vizhi.gurusamy

IEP

Co-expression (Functional linkage)
authors,DP. Pandey,K. Gerdes Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res. 2005

Citation

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

vizhi.gurusamy

IEP

15993073

Co-expression (Functional linkage)

Interaction

Inhibits Rv2757c

vizhi.gurusamy

IEP

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

Symbol

VapB21

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:3070849

rslayden

MTCY48.05c (72 aa), FASTA scores: opt: 106, E(): 0.52, (39.15% identity in 46 aa overlap); O06565

Other

strand:+

rslayden

MTCY48.05c (72 aa), FASTA scores: opt: 106, E(): 0.52, (39.15% identity in 46 aa overlap); O06565

Symbol

Vap BC-21

rslayden

Rv1113

Other

start:3070583

rslayden

Rv1113

Other

stop:3070849

rslayden

Rv1113

Other

strand:+

rslayden

Rv1113

Symbol

Vap BC-21

rslayden

MTCY22G8.02 (65 aa), FASTA scores: opt: 97, E(): 2.2, (33.35% identity in 69 aa overlap); etc. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp signature.

Other

start:3070583

rslayden

MTCY22G8.02 (65 aa), FASTA scores: opt: 97, E(): 2.2, (33.35% identity in 69 aa overlap); etc. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp signature.

Other

stop:3070849

rslayden

MTCY22G8.02 (65 aa), FASTA scores: opt: 97, E(): 2.2, (33.35% identity in 69 aa overlap); etc. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp signature.

Other

strand:+

rslayden

MTCY22G8.02 (65 aa), FASTA scores: opt: 97, E(): 2.2, (33.35% identity in 69 aa overlap); etc. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp signature.

Symbol

Vap BC-21

rslayden

Conserved hypothetical protein, similar to several other M. tuberculosis hypothetical proteins e.g. P95008

Other

start:3070583

rslayden

Conserved hypothetical protein, similar to several other M. tuberculosis hypothetical proteins e.g. P95008

Other

stop:3070849

rslayden

Conserved hypothetical protein, similar to several other M. tuberculosis hypothetical proteins e.g. P95008

Other

strand:+

rslayden

Conserved hypothetical protein, similar to several other M. tuberculosis hypothetical proteins e.g. P95008

Symbol

Vap BC-21

rslayden

Rv2545 (92 aa), FASTA scores: opt: 151, E(): 0.00028, (66.65%identity in 45 aa overlap); Q10771

Other

start:3070583

rslayden

Rv2545 (92 aa), FASTA scores: opt: 151, E(): 0.00028, (66.65%identity in 45 aa overlap); Q10771

Other

stop:3070849

rslayden

Rv2545 (92 aa), FASTA scores: opt: 151, E(): 0.00028, (66.65%identity in 45 aa overlap); Q10771

Other

strand:+

rslayden

Rv2545 (92 aa), FASTA scores: opt: 151, E(): 0.00028, (66.65%identity in 45 aa overlap); Q10771

Symbol

Vap BC-21

rslayden

YF60_MYCTU

Other

start:3070583

rslayden

YF60_MYCTU

Other

stop:3070849

rslayden

YF60_MYCTU

Other

strand:+

rslayden

YF60_MYCTU

Symbol

Vap BC-21

rslayden

Rv1560

Other

start:3070583

rslayden

Rv1560

Other

stop:3070849

rslayden

Rv1560

Other

strand:+

rslayden

Rv1560

Symbol

Vap BC-21

rslayden

MT1611

Other

start:3070583

rslayden

MT1611

Other

stop:3070849

rslayden

MT1611

Other

strand:+

rslayden

MT1611

Symbol

Vap BC-21

rslayden

MTCY48.05c (72 aa), FASTA scores: opt: 106, E(): 0.52, (39.15% identity in 46 aa overlap); O06565

Other

start:3070583

rslayden

MTCY48.05c (72 aa), FASTA scores: opt: 106, E(): 0.52, (39.15% identity in 46 aa overlap); O06565

Comments