Rv2052c (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: hypothetical protein
- PATRIC: Exoenzymes regulatory protein AepA in lipid-linked oligosaccharide synthesis cluster
- TUBERCULIST: Conserved protein
- NCBI: hypothetical protein
- updated information (H37Rv4):
  - gene name: -
  - function:
  - reference:
Type: Not Target
Start: 2310913
End: 2312517
Operon:

Trans-membrane region:
Role: VI - Unknowns
GO terms:
- GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005829 - cytosol (Uniprot)
- GO:0005618 - cell wall (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 Rv2052c:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 1.107 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VSQIPVKLLVNGRVYSPTHPEATAMAVRGDVVAWLGSDDVGRDQFPDADVQDLDGRFVAPGFVDSHIHLTATGLMLSGLDLRPATSRAQCLRMVADYAAD
HPGQPLWGHGWDESAWPENAAPSTADLDAVLGDCPAYLARIDSHSALVSSGLRRLVPELAAATGYTAQRPLTGDAHHLARAAARYLLTDVQLADARAVAL
QAIAAAGVVAVHECAGPEIGGLDDWLRLRALEHGVEVIGYWGEAVATPAQARDLVTETGARGLAGDLFVDGALGSRTAWLHEPYADAPDCIGTCHLDVDG
IEAHVRACTKAEVTAGFHVIGDAAVSAAVAAFERVVADLGVVAVARCGHRLEHVEMVTADQAAKLGAWGVIASVQPNFDELWGGGDGMYARRLGAQRGSE
LNPLALLASQGVPLALGSDAPVTGFDPWASVRAAVNHRTPGSGVSARAAFAAATRGGWRAGGVRDGRIGTLVPGAPASYAIWDAGDFDVDAPRDAVQRWS
TDPRSRVPALPRLGPTDALPRCRQTVHRGAVIYG

(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; 3 non-insertions in a row out of 21 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 21 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 21 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 22 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 22 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: 1.27
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:
- Rv0023 (-)
- Rv1221 (sigE)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv1049 (-) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv1221 (sigE)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0023 (-)

Property	Value	Creator	Evidence	PMID	Comment
Citation	The three RelE homologs of Mycobacterium tuberculosis have individual, drug-specific effects on bacterial antibiotic tolerance. authors,R. Singh,CE. Barry,HI. Boshoff J. Bacteriol. 2010	shahanup86	TAS	20061486	Co-expression (Functional linkage)
Interaction	Regulatory Rv1246c	shahanup86	TAS		Co-expression (Functional linkage) authors,R. Singh,CE. Barry,HI. Boshoff The three RelE homologs of Mycobacterium tuberculosis have individual, drug-specific effects on bacterial antibiotic tolerance. J. Bacteriol. 2010
Interaction	Regulatory Rv2866	shahanup86	TAS		Co-expression (Functional linkage) authors,R. Singh,CE. Barry,HI. Boshoff The three RelE homologs of Mycobacterium tuberculosis have individual, drug-specific effects on bacterial antibiotic tolerance. J. Bacteriol. 2010
Citation	The three RelE homologs of Mycobacterium tuberculosis have individual, drug-specific effects on bacterial antibiotic tolerance. authors,R. Singh,CE. Barry,HI. Boshoff J. Bacteriol. 2010	shahanup86	TAS	20061486	Operon (Functional linkage)
Interaction	PhysicalInteraction Rv2053c	shahanup86	TAS		Operon (Functional linkage) authors,R. Singh,CE. Barry,HI. Boshoff The three RelE homologs of Mycobacterium tuberculosis have individual, drug-specific effects on bacterial antibiotic tolerance. J. Bacteriol. 2010
Interaction	RegulatedBy Rv1221	yamir.moreno	IEP		Microarrays. mRNA levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using microarray (or macroarray) experiments.. R. Manganelli, MI. Voskuil et al. The Mycobacterium tuberculosis ECF sigma factor sigmaE: role in global gene expression and survival in macrophages. Mol. Microbiol. 2001

TB Genome Annotation Portal