Rv2527 (vapC17)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: toxin
- REFSEQ: hypothetical protein
- PATRIC: FIG00821417: hypothetical protein
- TUBERCULIST: Possible toxin VapC17
- NCBI: Possible toxin VapC17
- updated information (H37Rv4):
  - gene name: vapC17
  - function:
  - reference:
Type: Not Target
Start: 2851315
End: 2851716
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0090501 - RNA phosphodiester bond hydrolysis (Uniprot)
- GO:0090305 - nucleic acid phosphodiester bond hydrolysis (Uniprot)
- GO:0046872 - metal ion binding (Uniprot)
- GO:0016787 - hydrolase activity (Uniprot)
- GO:0004540 - ribonuclease activity (Uniprot)
- GO:0004518 - nuclease activity (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 vapC17:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 1.114 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MTTWILDKSAHVRLVAGATPPAGIDLTDLAICDIGELEWLYSARSATDYDSQQTSLRAYQILRAPSDIFDRVRHLQRDLAHHRGMWHRTPLPDLFIAETA
LHHRAGVLHHDRDYKRIAVVRPGFQACELSRGR

(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
Non-Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 9 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 9 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 9 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 10 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 10 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: 1.7
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:
- Rv0081 (-) (Upstream of operon)
- Rv0767c (-) (Upstream of operon)
- Rv1033c (trcR) (Upstream of operon)
- Rv1423 (whiA) (Upstream of operon)
- Rv1719 (-) (Upstream of operon)
- Rv2324 (-) (Upstream of operon)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv3260c (whiB2)
Downregulates:
- Does not downregulate other genes.
Downregulated by:

TBCAP

Tubculosis Community Annotation Project (

Slayden et al., 2013

Rv2527 (vapC17)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	InhibitedBy Rv2526	kandarpbioinfo	ISA		Gene neighbourhood 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	The PIN-domain toxin-antitoxin array in mycobacteria. authors,VL. Arcus,PB. Rainey,SJ. Turner Trends Microbiol. 2005	soumisengupta	NAS	15993073	Co-expression (Functional linkage)
Interaction	Inhibition Rv2526	soumisengupta	NAS		Co-expression (Functional linkage) authors,VL. Arcus,PB. Rainey,SJ. Turner The PIN-domain toxin-antitoxin array in mycobacteria. Trends Microbiol. 2005
Citation	Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. authors,A. Gupta FEMS Microbiol. Lett. 2009	soumisengupta	NAS	19016878	Co-expression (Functional linkage)
Interaction	Inhibition Rv2526	soumisengupta	NAS		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
Interaction	InhibitedBy Rv2526	kandarpbioinfo	ISA		Gene neighbourhood authors,VL. Arcus,PB. Rainey,SJ. Turner The PIN-domain toxin-antitoxin array in mycobacteria. Trends Microbiol. 2005
Interaction	InhibitedBy Rv2526	kandarpbioinfo	ISA		Gene neighbourhood 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	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	jlew		20011113	VapC homolog, PIN domain, Not toxic when expressed in Msmeg
Symbol	VapC17	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	start:2851315	rslayden			MTCY159.10c
Other	stop:2851716	rslayden			MTCY159.10c
Other	strand:+	rslayden			MTCY159.10c
Other	start:2851315	rslayden			Rv2546 (137 aa), FASTA scores: opt: 206, E(): 1.4e-07, (38.0% identity in 100 aa overlap); O33299
Other	stop:2851716	rslayden			Rv2546 (137 aa), FASTA scores: opt: 206, E(): 1.4e-07, (38.0% identity in 100 aa overlap); O33299
Other	strand:+	rslayden			Rv2546 (137 aa), FASTA scores: opt: 206, E(): 1.4e-07, (38.0% identity in 100 aa overlap); O33299
Other	start:2851315	rslayden			MTV002.22c
Other	stop:2851716	rslayden			MTV002.22c
Other	strand:+	rslayden			MTV002.22c
Other	start:2851315	rslayden			Rv2757c (138 aa), FASTA scores: opt: 201, E(): 3.1e-07, (35.7% identity in 126 aa overlap); and P96411
Other	stop:2851716	rslayden			Rv2757c (138 aa), FASTA scores: opt: 201, E(): 3.1e-07, (35.7% identity in 126 aa overlap); and P96411
Other	strand:+	rslayden			Rv2757c (138 aa), FASTA scores: opt: 201, E(): 3.1e-07, (35.7% identity in 126 aa overlap); and P96411
Other	start:2851315	rslayden			MTCY08D5.24c
Other	stop:2851716	rslayden			MTCY08D5.24c
Other	strand:+	rslayden			MTCY08D5.24c
Other	start:2851315	rslayden			Rv0229c (226 aa), FASTA scores: opt: 153, E(): 0.0011, (32.8% identity in 128 aa overlap).
Other	stop:2851716	rslayden			Rv0229c (226 aa), FASTA scores: opt: 153, E(): 0.0011, (32.8% identity in 128 aa overlap).
Other	strand:+	rslayden			Rv0229c (226 aa), FASTA scores: opt: 153, E(): 0.0011, (32.8% identity in 128 aa overlap).
Other	start:2851315	rslayden			Hypothetical protein, showing some similarity to hypothetical proteins from Mycobacterium tuberculosis e.g. P95007
Other	stop:2851716	rslayden			Hypothetical protein, showing some similarity to hypothetical proteins from Mycobacterium tuberculosis e.g. P95007
Other	strand:+	rslayden			Hypothetical protein, showing some similarity to hypothetical proteins from Mycobacterium tuberculosis e.g. P95007

Property

Value

Creator

Evidence

PMID

Comment

Interaction

InhibitedBy Rv2526

kandarpbioinfo

ISA

Gene neighbourhood
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

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

soumisengupta

NAS

15993073

Co-expression (Functional linkage)

Interaction

Inhibition Rv2526

soumisengupta

NAS

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

Citation

Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. authors,A. Gupta FEMS Microbiol. Lett. 2009

soumisengupta

NAS

19016878

Co-expression (Functional linkage)

Interaction

Inhibition Rv2526

soumisengupta

NAS

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

Interaction

InhibitedBy Rv2526

kandarpbioinfo

ISA

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

Interaction

InhibitedBy Rv2526

kandarpbioinfo

ISA

Gene neighbourhood
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

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

jlew

20011113

VapC homolog, PIN domain, Not toxic when expressed in Msmeg

Symbol

VapC17

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

start:2851315

rslayden

MTCY159.10c

Other

stop:2851716

rslayden

MTCY159.10c

Other

strand:+

rslayden

MTCY159.10c

Other

start:2851315

rslayden

Rv2546 (137 aa), FASTA scores: opt: 206, E(): 1.4e-07, (38.0% identity in 100 aa overlap); O33299

Other

stop:2851716

rslayden

Rv2546 (137 aa), FASTA scores: opt: 206, E(): 1.4e-07, (38.0% identity in 100 aa overlap); O33299

Other

strand:+

rslayden

Rv2546 (137 aa), FASTA scores: opt: 206, E(): 1.4e-07, (38.0% identity in 100 aa overlap); O33299

Other

start:2851315

rslayden

MTV002.22c

Other

stop:2851716

rslayden

MTV002.22c

Other

strand:+

rslayden

MTV002.22c

Other

start:2851315

rslayden

Rv2757c (138 aa), FASTA scores: opt: 201, E(): 3.1e-07, (35.7% identity in 126 aa overlap); and P96411

Other

stop:2851716

rslayden

Rv2757c (138 aa), FASTA scores: opt: 201, E(): 3.1e-07, (35.7% identity in 126 aa overlap); and P96411

Other

strand:+

rslayden

Rv2757c (138 aa), FASTA scores: opt: 201, E(): 3.1e-07, (35.7% identity in 126 aa overlap); and P96411

Other

start:2851315

rslayden

MTCY08D5.24c

Other

stop:2851716

rslayden

MTCY08D5.24c

Other

strand:+

rslayden

MTCY08D5.24c

Other

start:2851315

rslayden

Rv0229c (226 aa), FASTA scores: opt: 153, E(): 0.0011, (32.8% identity in 128 aa overlap).

Other

stop:2851716

rslayden

Rv0229c (226 aa), FASTA scores: opt: 153, E(): 0.0011, (32.8% identity in 128 aa overlap).

Other

strand:+

rslayden

Rv0229c (226 aa), FASTA scores: opt: 153, E(): 0.0011, (32.8% identity in 128 aa overlap).

Other

start:2851315

rslayden

Hypothetical protein, showing some similarity to hypothetical proteins from Mycobacterium tuberculosis e.g. P95007

Other

stop:2851716

rslayden

Hypothetical protein, showing some similarity to hypothetical proteins from Mycobacterium tuberculosis e.g. P95007

Other

strand:+

rslayden

Hypothetical protein, showing some similarity to hypothetical proteins from Mycobacterium tuberculosis e.g. P95007

Comments