Rv3479 (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: hypothetical protein
- PATRIC: POSSIBLE TRANSMEMBRANE PROTEIN
- TUBERCULIST: Possible transmembrane protein
- NCBI: Possible transmembrane protein
- updated information (H37Rv4):
  - gene name: -
  - function:
  - reference:
Type: Not Target
Start: 3895820
End: 3898885
Operon:

Trans-membrane region:
Role: VI - Unknowns
GO terms:
- GO:0016787 - hydrolase activity (Uniprot)
- GO:0016042 - lipid catabolic process (Uniprot)
- GO:0016021 - integral component of membrane (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0008152 - metabolic process (Uniprot)
- GO:0006629 - lipid metabolic process (Uniprot)
- GO:0005887 - integral component of plasma membrane (Uniprot)
- GO:0005886 - plasma membrane (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 Rv3479:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 1.165 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MAGVTREINLLAQASQWRRLGGTFPTNSQLTNESAASLRLYAQLIDLLDMVVDVDILSGTSAGGINAALLASSRVTGSDLGGIRDLWLDLGALTELLRDP
RDKKTPSLLYGDERIFAALAKRLPKLATGPFPPTTFPEAARTPSTTLYITTTLLAGETSRFTDSFGTLVQDVDLRGLFTFTETDLARPDTAPALALAARS
SASFPLAFEPSFLPFTKGTAKKGEVPARPAMAPFTSLTRPHWVSDGGLLDNRPIGVLFKRIFDRPARRPVRRVLLFVVPSSGPAPDPMHEPPPDNVDEPL
GLIDGLLKGLAAVTTQSIAADLRAIRAHQDCMEARTDAKLRLAELAATLRNGTRLLTPSLLTDYRTREATKQAQTLTSALLRRLSTCPPESGPATESLPK
SWSAELTVGGDADKVCRQQITATILLSWSQPTAQPLPQSPAELARFGQPAYDLAKGCALTVIRAAFQLARSDADIAALAEVTEAIHRAWRPTASSDLSVL
VRTMCSRPAIRQGSLENAADQLAADYLQQSTVPGDAWERLGAALVNAYPTLTQLAASASADSGAPTDSLLARDHVAAGQLETYLSYLGTYPGRADDSRDA
PTMAWKLFDLATTQRAMLPADAEIEQGLELVQVSADTRSLLAPDWQTAQQKLTGMRLHHFGAFYKRSWRANDWMWGRLDGAGWLVHVLLDPRRVRWIVGE
RADTNGPQSGAQWFLGKLKELGAPDFPSPGYPLPAVGGGPAQHLTEDMLLDELGFLDDPAKPLPASIPWTALWLSQAWQQRVLEEELDGLANTVLDPQPG
KLPDWSPTSSRTWATKVLAAHPGDAKYALLNENPIAGETFASDKGSPLMAHTVAKAAATAAGAAGSVRQLPSVLKPPLITLRTLTLSGYRVVSLTKGIAR
STIIAGALLLVLGVAAAIQSVTVFGVTGLIAAGTGGLLVVLGTWQVSGRLLFALLSFSVVGAVLALATPVVREWLFGTQQQPGWVGTHAYWLGAQWWHPL
VVVGLIALVAIMIAAATPGRR

(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 39 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 39 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 39 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 39 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 39 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: 0.46
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:
- Rv0302 (-) (Direct binding)
- Rv0967 (csoR) (Direct binding)
- Rv1395 (-) (Direct binding)
- Rv1423 (whiA) (Direct binding)
- Rv1816 (-) (Direct binding)
- Rv2034 (-) (Direct binding)
- Rv3160c (-) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0324 (-)
- Rv0757 (phoP)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0491 (regX3)
- Rv0818 (-)

Property	Value	Creator	Evidence	PMID	Comment
Citation	The Mycobacterium tuberculosis phoPR operon is positively autoregulated in the virulent strain H37Rv. J. Gonzalo-Asensio, CY. Soto et al. J. Bacteriol. 2008	raj252000	IEP	18757548	Co-expression (Functional Linkage)
Interaction	Regulatory Rv0757	raj252000	IEP		Co-expression (Functional Linkage) J. Gonzalo-Asensio, CY. Soto et al. The Mycobacterium tuberculosis phoPR operon is positively autoregulated in the virulent strain H37Rv. J. Bacteriol. 2008
Interaction	RegulatedBy Rv0757	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.. SB. Walters, E. Dubnau et al. The Mycobacterium tuberculosis PhoPR two-component system regulates genes essential for virulence and complex lipid biosynthesis. Mol. Microbiol. 2006

TB Genome Annotation Portal