Rv3439c (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: hypothetical protein
- PATRIC: Conserved alanine and proline rich protein
- TUBERCULIST: Conserved hypothetical alanine and proline rich protein
- NCBI: Conserved hypothetical alanine and proline rich protein
- updated information (H37Rv4):
  - gene name: ppr2
  - function: interacts with rip1?
  - reference: Schneider (2013) PMID: 24218594
Type: Not Target
Start: 3858259
End: 3859662
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- No terms assigned.
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 Rv3439c:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.942 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VADRLNVAERLAEGRPAAEHTQSYVRACHLVGYQHPDLTAYPAQIHDWYGSEDGLDLHALDADCAQLRAAASVLMEALRMERSQVAVLAAAWTGSGADAA
VHFVQRHCETGNSVVTEVRAAAQRCESLRDNLWQLVDSKVATAIAIDERALAQRPAWLAAAEALTTEGADRPTAVEVVRQQIQPYVDDDVRNDWLTTMRS
TTAGVAASYDAVTDQLASAPRAHFEIPDDLGPGRQPSPASVPAQPSATAAITPAAALPPPDPVPAVTSRPVTPSDFGSAPGDGSATPAGVGSAGGFGDAG
GTGGLGGFAGLAGLANRIVDAVDSLLGSVAEQLGDPLAADNPPGAVDPFAEDAADNADDGDDAHPEEADEAAEPKEATEPDEADEVDDADESVPAERAQD
VAEEATLPPVAEPPPPAAPPVAEPPPPVAAPAPPGAPEPANGPSPEALSEGATPCEIAADELPQAGP

(Nucleotide sequence available on KEGG)

Additional Information

Ppr2
interacts with Rip1?
(Schneider et al, 2013, PNAS) http://www.ncbi.nlm.nih.gov/pubmed/24218594

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; 0 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: 1.6
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:

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0023 (-) (Upstream of operon)
- Rv1816 (-) (Upstream of operon)
- Rv3249c (-) (Upstream of operon)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0022c (whiB5)
- Rv3911 (sigM)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0078 (-)
- Rv3223c (sigH)

Property	Value	Creator	Evidence	PMID	Comment
Citation	Characterization of the Mycobacterium tuberculosis sigma factor SigM by assessment of virulence and identification of SigM-dependent genes. N. Agarwal, SC. Woolwine et al. Infect. Immun. 2007	ranjeetsingh	IEP	17088352	Co-expression(Functional Linkage)
Interaction	Regulatory Rv3911	ranjeetsingh	IEP		Co-expression(Functional Linkage) N. Agarwal, SC. Woolwine et al. Characterization of the Mycobacterium tuberculosis sigma factor SigM by assessment of virulence and identification of SigM-dependent genes. Infect. Immun. 2007
Interaction	RegulatedBy Rv3911	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.. S. Raman, X. Puyang et al. Mycobacterium tuberculosis SigM positively regulates Esx secreted protein and nonribosomal peptide synthetase genes and down regulates virulence-associated surface lipid synthesis. J. Bacteriol. 2006
Interaction	RegulatedBy Rv3911	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.. N. Agarwal, SC. Woolwine et al. Characterization of the Mycobacterium tuberculosis sigma factor SigM by assessment of virulence and identification of SigM-dependent genes. Infect. Immun. 2007

TB Genome Annotation Portal