Rv2595 (vapB40)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: antitoxin
- REFSEQ: hypothetical protein
- PATRIC: FIG00823117: hypothetical protein
- TUBERCULIST: Possible antitoxin VapB40
- NCBI: Possible antitoxin VapB40
- updated information (H37Rv4):
  - gene name: vapB40
  - function:
  - reference:
Type: Not Target
Start: 2925492
End: 2925737
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0005515 - protein binding (Uniprot)
- GO:0003677 - DNA 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): (none with >35% aa id)
Links to additional information on vapB40:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.517 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MRTTIDVAGRLVIPKRIRERLGLRGNDQVEITERDGRIEIEPAPTGVELVREGSVLVARPERPLPPLTDEIVRETLDRTRR

(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 0 sites
Too-Short	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 0 non-insertions in a row out of 0 sites
Too-Short	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 0 non-insertions in a row out of 0 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: 0.62
Uncertain	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

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

Binds To:
- Rv2595 (vapB40) (Direct binding)
- Rv2596 (vapC40) (Upstream of operon)
Bound By:
- Rv0081 (-) (Direct binding)
- Rv1423 (whiA) (Direct binding)
- Rv2595 (vapB40) (Direct binding)
- Rv3736 (-) (Direct binding)

Property	Value	Creator	Evidence	PMID	Comment
Citation	The vapBC operon from Mycobacterium smegmatis is an autoregulated toxin-antitoxin module that controls growth via inhibition of translation. authors,J. Robson,JL. McKenzie,R. Cursons,GM. Cook,VL. Arcus J. Mol. Biol. 2009	xaccheus	TAS	19445953	Structural Analysis
Interaction	Operon Rv2596	xaccheus	TAS		Structural Analysis authors,J. Robson,JL. McKenzie,R. Cursons,GM. Cook,VL. Arcus The vapBC operon from Mycobacterium smegmatis is an autoregulated toxin-antitoxin module that controls growth via inhibition of translation. J. Mol. Biol. 2009
Interaction	Operon Rv2596	xaccheus	TAS		Spectrophotometric authors,VL. Arcus,K. Bckbro,A. Roos,EL. Daniel,EN. Baker Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease. J. Biol. Chem. 2004
Interaction	Operon Rv2596	xaccheus	TAS		Structural Analysis authors,VL. Arcus,K. Bckbro,A. Roos,EL. Daniel,EN. Baker Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease. J. Biol. Chem. 2004
Citation	The PIN-domain toxin-antitoxin array in mycobacteria. authors,VL. Arcus,PB. Rainey,SJ. Turner Trends Microbiol. 2005	xaccheus	TAS	15993073	Spectrophotometric
Interaction	Operon Rv2596	xaccheus	TAS		Spectrophotometric authors,VL. Arcus,PB. Rainey,SJ. Turner The PIN-domain toxin-antitoxin array in mycobacteria. Trends Microbiol. 2005
Citation	The vapBC operon from Mycobacterium smegmatis is an autoregulated toxin-antitoxin module that controls growth via inhibition of translation. authors,J. Robson,JL. McKenzie,R. Cursons,GM. Cook,VL. Arcus J. Mol. Biol. 2009	xaccheus	TAS	19445953	Spectrophotometric
Interaction	Operon Rv2596	xaccheus	TAS		Spectrophotometric authors,J. Robson,JL. McKenzie,R. Cursons,GM. Cook,VL. Arcus The vapBC operon from Mycobacterium smegmatis is an autoregulated toxin-antitoxin module that controls growth via inhibition of translation. J. Mol. Biol. 2009
Citation	The PIN-domain toxin-antitoxin array in mycobacteria. authors,VL. Arcus,PB. Rainey,SJ. Turner Trends Microbiol. 2005	xaccheus	TAS	15993073	Structural Analysis
Interaction	Operon Rv2596	xaccheus	TAS		Structural Analysis authors,VL. Arcus,PB. Rainey,SJ. Turner The PIN-domain toxin-antitoxin array in mycobacteria. Trends Microbiol. 2005
Symbol	vapB-mt25	jlew			No growth when mazF-mt1 expressed in Ecoli but restored when mazE-mt1 was co-induced. mazF-mt1 could also be partially neutralized by vapB-mt24 or vapB-mt25. Growth inhibition by mazF-mt3; normal growth if mazE-mt1, mazE-mt3, vapB-mt24 or vapB-mt25 were co-expressed. Each pair shows interaction by pull-down. authors,L. Zhu,JD. Sharp,H. Kobayashi,NA. Woychik,M. Inouye Noncognate Mycobacterium tuberculosis toxin-antitoxins can physically and functionally interact. J. Biol. Chem. 2010
Citation	Noncognate Mycobacterium tuberculosis toxin-antitoxins can physically and functionally interact. authors,L. Zhu,JD. Sharp,H. Kobayashi,NA. Woychik,M. Inouye J. Biol. Chem. 2010	jlew		20876537	No growth when mazF-mt1 expressed in Ecoli but restored when mazE-mt1 was co-induced. mazF-mt1 could also be partially neutralized by vapB-mt24 or vapB-mt25. Growth inhibition by mazF-mt3; normal growth if mazE-mt1, mazE-mt3, vapB-mt24 or vapB-mt25 were co-expressed. Each pair shows interaction by pull-down.

TB Genome Annotation Portal

Rv2595 (vapB40)

Amino Acid Sequence

Additional Information

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