Rv3267 (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: hypothetical protein
- PATRIC: Cell envelope-associated transcriptional attenuator LytR-CpsA-Psr subfamily A1 (as in PMID19099556)
- TUBERCULIST: Conserved protein (CPSA-related protein)
- NCBI: Conserved protein (CPSA-related protein)
- updated information (H37Rv4):
  - gene name: lcp1
  - function: PG-AG ligase (peptidoglycan-arabinogalactan)
  - reference: Harrison (2016) PMID: 27486192
Type: Essential
Start: 3647885
End: 3649381
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0040007 - growth (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005576 - extracellular region (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 Rv3267:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.614 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology
- Photo of spot titer

Amino Acid Sequence

VMSAQRVVRTVRTARAISTALAVAIVLGTGVAWSSVRSFEDGIFHMSAPSLGHGGDDGAIDILLVGLDSRTDAHGNPLSAEELATLHAGDEEATNTDTII
LIRVPNNGKSATAISIPRDSYVAAPGLGKTKINGVYGQTRETKRAGLVQAGASPTEAAAAGTEAGREALIKTVADLTGVTVDHYAEIGLLGFALIADALG
GVDVCLKEPVYEPLSGADFPAGRQKLNGPQALSFVRQRHDLPRGDLDRVVRQQAVMAALAHRVISGQTLSSPATLKRLEQAVQRSVVLSSGWDIMDFVRQ
LQKLAGGNVAFATIPVLDGAGWSDDGMQSVVRVDPRQVQDWVVGLLHEQDQGKTDELAYTPAKTTANVVNDTDINGLAAAVSKVLSSKGFTTGSVGNNDG
DHVPGSQVRAAKADDLGAQQVAKELGGLPVVADASIAPGSVRVVLANDYSGPGSGLGGSDPNGVVSPARAFNLGSADDTTPPPSPILTAGSDAPECIN

(Nucleotide sequence available on KEGG)

Additional Information

Lcp1 - PG-AG ligase (peptidoglycan-arabinogalactan ligase)
Harrison et al (2016). Lcp1 Is a Phosphotransferase Responsible for Ligating Arabinogalactan to Peptidoglycan in Mycobacterium tuberculosis. mBio. http://mbio.asm.org/content/7/4/e00972-16.abstract

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
Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 23 non-insertions in a row out of 23 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 15 non-insertions in a row out of 23 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 23 non-insertions in a row out of 23 sites
Uncertain	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.882400; 8 non-insertions in a row out of 23 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.999900; 14 non-insertions in a row out of 23 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.1
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:
- Rv0135c (-) (Direct binding)
- Rv2250c (-) (Direct binding)

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:

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Regulatory Rv3269	vashishtrv	IEP		Co-expression (Functional linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Interaction	Regulatory Rv3268	shahanup86	IEP		Co-expression (Functional linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Interaction	Regulatory Rv3268	vashishtrv	IEP		Co-expression (Functional linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Citation	Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. S. Raman, R. Hazra et al. J. Bacteriol. 2004	shahanup86	IEP	15375142	Co-expression (Functional linkage)
Interaction	Regulatory Rv3268	shahanup86	IEP		Co-expression (Functional linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Interaction	Regulatory Rv3269	shahanup86	IEP		Co-expression (Functional linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Citation	Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. S. Raman, R. Hazra et al. J. Bacteriol. 2004	vashishtrv	IEP	15375142	Co-expression (Functional linkage)
Interaction	Regulatory Rv3268	vashishtrv	IEP		Co-expression (Functional linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Interaction	RegulatedBy Rv2069	yamir.moreno	TAS		Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008

TB Genome Annotation Portal