Rv1195 (PE13)
Current annotations:
TBCAP: (community-based annotations - see table at bottom of page )
TBDB: hypothetical protein
REFSEQ: PE family protein
PATRIC: FIG018298: PE family protein
TUBERCULIST: PE family protein PE13
NCBI: PE family protein PE13
updated information (H37Rv4):
gene name: PE13
function:
reference:
Type: Not Target
Start: 1339003
End: 1339302
Operon:
Trans-membrane region:
Role: IV.C.1.a - PE subfamily
GO terms:
Reaction(s) (based on iSM810 metabolic model):
Gene Expression Profile Gene Modules 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 5XFS 56% Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) Crystal structure of PE8-PPE15 in complex with EspG5 from M. tuberculosis
Links to additional information on PE13:
Amino Acid Sequence
VSFVMAYPEMLAAAADTLQSIGATTVASNAAAAAPTTGVVPPAADEVSALTAAHFAAHAAMYQSVSARAAAIHDQFVATLASSASSYAATEVANAAAAS
(
Nucleotide sequence available on
KEGG )
Additional Information
Analysis of Positive Selection in Clinical Isolates
*new*
Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods )
Moldova: 2,057 clinical isolates
global set: 5,195 clinical isolates from 15 other countries
In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.
Moldova (2,057) global set (5,195)
under significant positive selection? NO NO
omega peak height (95%CI lower bound) 1.11 (0.05) 1.83 (0.63)
codons under selection
omega plots
genetic variants* link link
statistics at each codon link link
* example format for variants: "D27 (GAC): D27H (CAC,11)" means "Asp27 (native codon GAC) mutated to His (codon CAC) in 11 isolates"
MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb
TnSeqCorr
Rv1195/PE13,
gene len: 299 bp, num TA sites: 6
condition dataset call medium method notes
in-vitro DeJesus 2017 mBio growth advantage 7H9 HMM fully saturated, 14 TnSeq libraries combined
in-vitro Sassetti 2003 Mol Micro no data 7H9 TRASH essential if hybridization ratio<0.2
in-vivo (mice) Sassetti 2003 PNAS non-essential BL6 mice TRASH essential if hybridization ratio<0.4, min over 4 timepoints (1-8 weeks)
in-vitro (glycerol) Griffin 2011 PPath non-essential M9 minimal+glycerol Gumbel 2 replicates; Padj<0.05
in-vitro (cholesterol) Griffin 2011 PPath non-essential M9 minimal+cholesterol Gumbel 3 replicates; Padj<0.05
differentially essential in cholesterol Griffin 2011 PPath NO (LFC=-0.55) cholesterol vs glycerol resampling-SR YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in cholesterol
in-vitro Smith 2022 eLife non-essential 7H9 HMM 6 replicates (raw data in Subramaniam 2017, PMID 31752678)
in-vivo (mice) Smith 2022 eLife non-essential BL6 mice HMM 6 replicates (raw data in Subramaniam 2017, PMID 31752678)
differentially essential in mice Smith 2022 eLife NO (LFC=0.55) in-vivo vs in-vitro ZINB YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in mice
in-vitro (minimal) Minato 2019 mSys non-essential minimal medium HMM
in-vitro (YM rich medium) Minato 2019 mSys non-essential YM rich medium HMM 7H9 supplemented with ~20 metabolites (amino acids, cofactors)
differentially essential in YM rich medium Minato 2019 mSys NO (LFC=-0.17) YM rich vs minimal medium resampling
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
Translation, ribosomal structure and biogenesis
Cell wall/membrane/envelope biogenesis
Replication, recombination and repair
Posttranslational modification, protein turnover, chaperones
Secondary metabolites biosynthesis, transport and catabolism
Inorganic ion transport and metabolism
General function prediction only
Intracellular trafficking, secretion, and vesicular transport
Signal transduction mechanisms
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).
Binds To:
No bindings to other targets were found.
Bound By:
No bindings from other targets were found.
Binds To:
No bindings to other targets were found.
Bound By:
No bindings to other targets were found.
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 Transcription Rv2359 ahal4789 IDA Band shiftA. Maciag, E. Dainese et al. Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. J. Bacteriol. 2007
Citation Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate. S. Denkin, S. Byrne et al. Arch. Microbiol. 2005 ahal4789 IDA 16175359 Band shift
Interaction Transcription Rv2359 ahal4789 IDA Band shiftS. Denkin, S. Byrne et al. Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate. Arch. Microbiol. 2005
Citation The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. RM. Goldstone, SD. Goonesekera et al. Infect. Immun. 2009 ahal4789 IEP 19651861 Co-expression (Functional linkage)
Interaction Regulatory Rv0485 ahal4789 IEP Co-expression (Functional linkage)RM. Goldstone, SD. Goonesekera et al. The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. Infect. Immun. 2009
Citation The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. RM. Goldstone, SD. Goonesekera et al. Infect. Immun. 2009 ahal4789 TAS 19651861 None
Interaction PhysicalInteraction Rv1196 ahal4789 TAS RM. Goldstone, SD. Goonesekera et al. The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. Infect. Immun. 2009
Citation Differential expression of PE and PE_PGRS genes in Mycobacterium tuberculosis strains. J. Flores & C. Espitia Gene 2003 ahal4789 NAS 14585500 None
Interaction Regulatory Rv0279c ahal4789 NAS J. Flores & C. Espitia Differential expression of PE and PE_PGRS genes in Mycobacterium tuberculosis strains. Gene 2003
Citation Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate. S. Denkin, S. Byrne et al. Arch. Microbiol. 2005 ahal4789 NAS 16175359 None
Interaction Regulatory Rv0279c ahal4789 NAS S. Denkin, S. Byrne et al. Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate. Arch. Microbiol. 2005
Citation Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. A. Maciag, E. Dainese et al. J. Bacteriol. 2007 ahal4789 IDA 17098899 Band shift
Interaction Regulatory Rv0485 yashabhasin IMP Affinity purification (Physical interaction)RM. Goldstone, SD. Goonesekera et al. The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. Infect. Immun. 2009
Interaction RegulatedBy Rv0485 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.. qRT-PCR. mRNA expression levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using qRT-PCR technique.RM. Goldstone, SD. Goonesekera et al. The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. Infect. Immun. 2009
Interaction RegulatedBy Rv0485 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.. qRT-PCR. mRNA expression levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using qRT-PCR technique.RM. Goldstone, SD. Goonesekera et al. The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. Infect. Immun. 2009
Interaction RegulatedBy Rv0981 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..H. He, R. Hovey et al. MprAB is a stress-responsive two-component system that directly regulates expression of sigma factors SigB and SigE in Mycobacterium tuberculosis. J. Bacteriol. 2006
Interaction RegulatedBy Rv2359 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..A. Maciag, E. Dainese et al. Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. J. Bacteriol. 2007
Interaction RegulatedBy Rv2359 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
Interaction RegulatedBy Rv3286c 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.. qRT-PCR. mRNA expression levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using qRT-PCR technique.EP. Williams, JH. Lee et al. Mycobacterium tuberculosis SigF regulates genes encoding cell wall-associated proteins and directly regulates the transcriptional regulatory gene phoY1. J. Bacteriol. 2007
Interaction RegulatedBy Rv3286c 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.. qRT-PCR. mRNA expression levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using qRT-PCR technique.EP. Williams, JH. Lee et al. Mycobacterium tuberculosis SigF regulates genes encoding cell wall-associated proteins and directly regulates the transcriptional regulatory gene phoY1. J. Bacteriol. 2007
Interaction RegulatedBy Rv0491 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..T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003
Citation The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. RM. Goldstone, SD. Goonesekera et al. Infect. Immun. 2009 jlew 19651861 reduced expression in Rv0485 mutant. Defined the Rv0485 regulon
Citation Mycobacterium tuberculosis SigF regulates genes encoding cell wall-associated proteins and directly regulates the transcriptional regulatory gene phoY1. EP. Williams, JH. Lee et al. J. Bacteriol. 2007 jlew 17384187 We found that overexpression of sigF resulted in the differential regulation of many cell wall-associated proteins, including members of the MmpL, PE, and PPE families.
