Rv1368 (lprF)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: lipoprotein lprF
- REFSEQ: lipoprotein LprF
- PATRIC: Lipoprotein LprF
- TUBERCULIST: Probable conserved lipoprotein LprF
- NCBI: Probable conserved lipoprotein LprF
- updated information (H37Rv4):
  - gene name: lprF
  - function:
  - reference:
Type: Not Target
Start: 1541020
End: 1541805
Operon:

Trans-membrane region:
Role: II.C.1 - Lipoproteins(lppA-lpr0)
GO terms:
- GO:0016020 - membrane (Uniprot)
- GO:0008289 - lipid binding (Uniprot)
- GO:0006869 - lipid transport (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005618 - cell wall (Uniprot)
- GO:0005576 - extracellular region (Uniprot)
- GO:0005515 - protein binding (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):

PDB aa ident species PDB title

4QA8 100% Mycobacterium bovis Crystal structure of LprF from Mycobacterium bovis
Links to additional information on lprF:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 1.022 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

PDB	aa ident	species	PDB title
4QA8	100%	Mycobacterium bovis	Crystal structure of LprF from Mycobacterium bovis

Amino Acid Sequence

MNGLISQACGSHRPRRPSSLGAVAILIAATLFATVVAGCGKKPTTASSPSPGSPSPEAQQILQDSSKATKGLHSVHVVVTVNNLSTLPFESVDADVTNQP
QGNGQAVGNAKVRMKPNTPVVATEFLVTNKTMYTKRGGDYVSVGPAEKIYDPGIILDKDRGLGAVVGQVQNPTIQGRDAIDGLATVKVSGTIDAAVIDPI
VPQLGKGGGRLPITLWIVDTNASTPAPAANLVRMVIDKDQGNVDITLSNWGAPVTIPNPAG

(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 7 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 7 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 7 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 8 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 8 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: 1.42
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

RNA processing and modification

Energy production and conversion

Chromatin structure and dynamics

Amino acid transport and metabolism

Cell cycle control, cell division, chromosome partitioning

Carbohydrate transport and metabolism

Nucleotide transport and metabolism

Lipid transport and metabolism

Coenzyme transport and metabolism

Transcription

Translation, ribosomal structure and biogenesis

Cell wall/membrane/envelope biogenesis

Replication, recombination and repair

Posttranslational modification, protein turnover, chaperones

Cell motility

Secondary metabolites biosynthesis, transport and catabolism

Inorganic ion transport and metabolism

Function unknown

General function prediction only

Intracellular trafficking, secretion, and vesicular transport

Signal transduction mechanisms

Extracellular structures

Defense mechanisms

Nuclear structure

Cytoskeleton

BioCyc Co-regulated genes based on gene expression profiling (Systems Biology, Inferelator Network)

Differentially expressed as result of RNASeq in glycerol environment (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

Conditionally essential as result of TNSeq (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

BioCyc Transcription factor binding based on ChIP-Seq (Systems Biology)

Binds To:
- No bindings to other targets were found.
Bound By:
- No bindings from other targets were found.

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0678 (-) (Direct binding)
- Rv0767c (-) (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:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Citation	Interaction of the sensor module of Mycobacterium tuberculosis H37Rv KdpD with members of the Lpr family. AJ. Steyn, J. Joseph et al. Mol. Microbiol. 2003	swetha.r	IPI	12581360	Yeast two-hybrid (Physical interaction)
Interaction	Regulatory Rv1028c	swetha.r	IPI		Yeast two-hybrid (Physical interaction) AJ. Steyn, J. Joseph et al. Interaction of the sensor module of Mycobacterium tuberculosis H37Rv KdpD with members of the Lpr family. Mol. Microbiol. 2003
Citation	Interaction of the sensor module of Mycobacterium tuberculosis H37Rv KdpD with members of the Lpr family. AJ. Steyn, J. Joseph et al. Mol. Microbiol. 2003	swetha.r	IPI	12581360	Yeast three-hybrid (Physical interaction)
Interaction	Regulatory Rv1028c	swetha.r	IPI		Yeast three-hybrid (Physical interaction) AJ. Steyn, J. Joseph et al. Interaction of the sensor module of Mycobacterium tuberculosis H37Rv KdpD with members of the Lpr family. Mol. Microbiol. 2003
Interaction	Signaling Rv1028c	darhngu	IPI		Yeast Two- Three Hybrid(Physical Interaction) T. Parish, DA. Smith et al. Deletion of two-component regulatory systems increases the virulence of Mycobacterium tuberculosis. Infect. Immun. 2003
Interaction	Signaling Rv1028c	darhngu	IPI		Yeast Two- Three Hybrid(Physical Interaction) A. Singh, D. Mai et al. Dissecting virulence pathways of Mycobacterium tuberculosis through protein-protein association. Proc. Natl. Acad. Sci. U.S.A. 2006
Interaction	Signaling Rv1028c	darhngu	IPI		Yeast Two- Three Hybrid(Physical Interaction) AJ. Steyn, J. Joseph et al. Interaction of the sensor module of Mycobacterium tuberculosis H37Rv KdpD with members of the Lpr family. Mol. Microbiol. 2003

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