Rv1838c (vapC13)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: toxin
- REFSEQ: hypothetical protein
- PATRIC: FIG00821467: hypothetical protein
- TUBERCULIST: Possible toxin VapC13
- NCBI: Possible toxin VapC13
- updated information (H37Rv4):
  - gene name: vapC13
  - function:
  - reference:
Type: Conditional
Start: 2087257
End: 2087652
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:0005576 - extracellular region (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 vapC13:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.332 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VILVDSNIPMYLVGASHPHKLDAQRLLESALSGGERLVTDAEVLQEICHRYVAIKRREAIQPAFDAIIGVVDEVLPIERTDVEHARDALLRYQTLSARDA
LHIAVMAHHDITRLMSFDRGFDSYPGIKRLA

(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; 1 non-insertions in a row out of 10 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 10 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 10 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 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; 0 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: 3.63
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:
- Rv0019c (fhaB)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0047c (-) (Direct binding)
- Rv0967 (csoR) (Upstream of operon)
- Rv1033c (trcR) (Upstream of operon)
- Rv2989 (-) (Upstream of operon)

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:
- Rv0019c (fhaB)

TBCAP

Tubculosis Community Annotation Project (

Slayden et al., 2013

Rv1838c (vapC13)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Regulatory Rv1839c	ilamathi.raja	ISA		Co-occurrence (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	Regulatory Rv1839c	ilamathi.raja	ISA		Co-occurrence (Functional linkage) authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009
Interaction	Regulatory Rv1839c	ilamathi.raja	ISA		Co-occurrence (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	Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. authors,A. Gupta FEMS Microbiol. Lett. 2009	ilamathi.raja	ISA	19016878	Co-occurrence (Functional linkage)
Interaction	Regulatory Rv1839c	ilamathi.raja	ISA		Co-occurrence (Functional linkage) authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 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	ilamathi.raja	ISA	20011113	Co-occurrence (Functional linkage)
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	VapC13	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:2087257	rslayden			Conserved hypothetical protein. Part of 14-membered Mycobacterium tuberculosis protein family with Rv2863
Other	stop:2087652	rslayden			Conserved hypothetical protein. Part of 14-membered Mycobacterium tuberculosis protein family with Rv2863
Other	strand:+	rslayden			Conserved hypothetical protein. Part of 14-membered Mycobacterium tuberculosis protein family with Rv2863
Other	start:2087257	rslayden			MTV003.09
Other	stop:2087652	rslayden			MTV003.09
Other	strand:+	rslayden			MTV003.09
Other	start:2087257	rslayden			AL008883 (126 aa), FASTA scores: opt: 293, E(): 1.5e-14, (38.2% identity in 123 aa overlap); Rv0749, Rv0277c, Rv2530c, etc. Also similar to AJ248288
Other	stop:2087652	rslayden			AL008883 (126 aa), FASTA scores: opt: 293, E(): 1.5e-14, (38.2% identity in 123 aa overlap); Rv0749, Rv0277c, Rv2530c, etc. Also similar to AJ248288
Other	strand:+	rslayden			AL008883 (126 aa), FASTA scores: opt: 293, E(): 1.5e-14, (38.2% identity in 123 aa overlap); Rv0749, Rv0277c, Rv2530c, etc. Also similar to AJ248288
Other	start:2087257	rslayden			CNSPAX06_181 Pyrococcus abyssi complete genome (136 aa), FASTA scores: opt: 197, E(): 2.2e-07, (33. 1% identity in 133 aa overlap).
Other	stop:2087652	rslayden			CNSPAX06_181 Pyrococcus abyssi complete genome (136 aa), FASTA scores: opt: 197, E(): 2.2e-07, (33. 1% identity in 133 aa overlap).
Other	strand:+	rslayden			CNSPAX06_181 Pyrococcus abyssi complete genome (136 aa), FASTA scores: opt: 197, E(): 2.2e-07, (33. 1% identity in 133 aa overlap).

Property

Value

Creator

Evidence

PMID

Comment

Interaction

Regulatory Rv1839c

ilamathi.raja

ISA

Co-occurrence (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

Regulatory Rv1839c

ilamathi.raja

ISA

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

Interaction

Regulatory Rv1839c

ilamathi.raja

ISA

Citation

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

ilamathi.raja

ISA

19016878

Co-occurrence (Functional linkage)

Interaction

Regulatory Rv1839c

ilamathi.raja

ISA

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

ilamathi.raja

ISA

20011113

Co-occurrence (Functional linkage)

Citation

jlew

20011113

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

Symbol

VapC13

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:2087257

rslayden

Conserved hypothetical protein. Part of 14-membered Mycobacterium tuberculosis protein family with Rv2863

Other

stop:2087652

rslayden

Conserved hypothetical protein. Part of 14-membered Mycobacterium tuberculosis protein family with Rv2863

Other

strand:+

rslayden

Conserved hypothetical protein. Part of 14-membered Mycobacterium tuberculosis protein family with Rv2863

Other

start:2087257

rslayden

MTV003.09

Other

stop:2087652

rslayden

MTV003.09

Other

strand:+

rslayden

MTV003.09

Other

start:2087257

rslayden

AL008883 (126 aa), FASTA scores: opt: 293, E(): 1.5e-14, (38.2% identity in 123 aa overlap); Rv0749, Rv0277c, Rv2530c, etc. Also similar to AJ248288

Other

stop:2087652

rslayden

AL008883 (126 aa), FASTA scores: opt: 293, E(): 1.5e-14, (38.2% identity in 123 aa overlap); Rv0749, Rv0277c, Rv2530c, etc. Also similar to AJ248288

Other

strand:+

rslayden

AL008883 (126 aa), FASTA scores: opt: 293, E(): 1.5e-14, (38.2% identity in 123 aa overlap); Rv0749, Rv0277c, Rv2530c, etc. Also similar to AJ248288

Other

start:2087257

rslayden

CNSPAX06_181 Pyrococcus abyssi complete genome (136 aa), FASTA scores: opt: 197, E(): 2.2e-07, (33. 1% identity in 133 aa overlap).

Other

stop:2087652

rslayden

CNSPAX06_181 Pyrococcus abyssi complete genome (136 aa), FASTA scores: opt: 197, E(): 2.2e-07, (33. 1% identity in 133 aa overlap).

Other

strand:+

rslayden

CNSPAX06_181 Pyrococcus abyssi complete genome (136 aa), FASTA scores: opt: 197, E(): 2.2e-07, (33. 1% identity in 133 aa overlap).

Comments