PePPER: a webserver for prediction of prokaryote promoter elements and regulons (Q34321949)

1 August 2017

title

PePPER: a webserver for prediction of prokaryote promoter elements and regulons (English)

1 reference

1 August 2017

Anne de Jong

1 reference

1 August 2017

Hilco Pietersma

1 reference

1 August 2017

Martijn Cordes

1 reference

1 August 2017

Oscar P Kuipers

1 reference

1 August 2017

Jan Kok

1 reference

1 August 2017

language of work or name

English

0 references

publication date

2 July 2012

1 reference

1 August 2017

1 reference

1 August 2017

1 reference

1 August 2017

page(s)

299

1 reference

The putative hydrolase YycJ (WalJ) affects the coordination of cell division with DNA replication in Bacillus subtilis and may play a conserved role in cell wall metabolism

1 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

FITBAR: a web tool for the robust prediction of prokaryotic regulons

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Localization and cellular amounts of the WalRKJ (VicRKX) two-component regulatory system proteins in serotype 2 Streptococcus pneumoniae.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Tmod: toolbox of motif discovery

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

MicrobesOnline: an integrated portal for comparative and functional genomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

MOODS: fast search for position weight matrix matches in DNA sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

MEME SUITE: tools for motif discovery and searching

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Structure of the transcriptional regulator LmrR and its mechanism of multidrug recognition

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

A matter of life and death: cell wall homeostasis and the WalKR (YycGF) essential signal transduction pathway

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

NCBI BLAST: a better web interface

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

LmrR is a transcriptional repressor of expression of the multidrug ABC transporter LmrCD in Lactococcus lactis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Characterization of the CopR regulon of Lactococcus lactis IL1403.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Lactococcus lactis, an efficient cell factory for recombinant protein production and secretion.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Osmotic regulation of transcription in Lactococcus lactis: ionic strength-dependent binding of the BusR repressor to the busA promoter.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Identifying bacterial genes and endosymbiont DNA with Glimmer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Substrate recognition by the hetero-octameric ATP phosphoribosyltransferase from Lactococcus lactis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Time-resolved determination of the CcpA regulon of Lactococcus lactis subsp. cremoris MG1363.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

GlnR-mediated regulation of nitrogen metabolism in Lactococcus lactis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Overall control of nitrogen metabolism in Lactococcus lactis by CodY, and possible models for CodY regulation in Firmicutes.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Specificity and selectivity determinants of peptide transport in Lactococcus lactis and other microorganisms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

The Lactococcus lactis CodY regulon: identification of a conserved cis-regulatory element.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Sulfur amino acid metabolism and its control in Lactococcus lactis IL1403.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Fructose utilization in Lactococcus lactis as a model for low-GC gram-positive bacteria: its regulator, signal, and DNA-binding site

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Two acid-inducible promoters from Lactococcus lactis require the cis-acting ACiD-box and the transcription regulator RcfB.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Interaction between ArgR and AhrC controls regulation of arginine metabolism in Lactococcus lactis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Probing direct interactions between CodY and the oppD promoter of Lactococcus lactis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

ArgR and AhrC are both required for regulation of arginine metabolism in Lactococcus lactis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Heat and DNA damage induction of the LexA-like regulator HdiR from Lactococcus lactis is mediated by RecA and ClpP.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Operon: a group of genes with the expression coordinated by an operator

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

ClpE from Lactococcus lactis promotes repression of CtsR-dependent gene expression

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Vienna RNA secondary structure server

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Physiological function of the maltose operon regulator, MalR, in Lactococcus lactis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Regulation of the metC-cysK operon, involved in sulfur metabolism in Lactococcus lactis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

The pyrimidine operon pyrRPB-carA from Lactococcus lactis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Dissolution of xylose metabolism in Lactococcus lactis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

ctsR of Lactococcus lactis encodes a negative regulator of clp gene expression.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Six putative two-component regulatory systems isolated from Lactococcus lactis subsp. cremoris MG1363.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

A transcriptional activator, homologous to the Bacillus subtilis PurR repressor, is required for expression of purine biosynthetic genes in Lactococcus lactis.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

A chloride-inducible gene expression cassette and its use in induced lysis of Lactococcus lactis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Molecular cloning and nucleotide sequence of the gene encoding the major peptidoglycan hydrolase of Lactococcus lactis, a muramidase needed for cell separation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

ARCS-Motif: discovering correlated motifs from unaligned biological sequences

6 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-299

GIMSAN: a Gibbs motif finder with significance analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-299

RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-299

GAME: detecting cis-regulatory elements using a genetic algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-299

A probabilistic method for identifying start codons in bacterial genomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-299

Osmoregulation in Lactococcus lactis: BusR, a transcriptional repressor of the glycine betaine uptake system BusA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-299

Identification and functional characterization of the Lactococcus lactis CodY-regulated branched-chain amino acid permease BcaP (CtrA).

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-299

Regulation of flpA, flpB and rcfA promoters in Lactococcus lactis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-299

A chloride-inducible acid resistance mechanism in Lactococcus lactis and its regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-299

The quaternary structure of the HisZ-HisG N-1-(5'-phosphoribosyl)-ATP transferase from Lactococcus lactis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-299

Cell envelope stress induced by the bacteriocin Lcn972 is sensed by the Lactococcal two-component system CesSR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-299

Inactivation of a gene that is highly conserved in Gram-positive bacteria stimulates degradation of non-native proteins and concomitantly increases stress tolerance in Lactococcus lactis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-299

Essentiality, bypass, and targeting of the YycFG (VicRK) two-component regulatory system in gram-positive bacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-299

Inactivation of the Lactococcus lactis high-affinity phosphate transporter confers oxygen and thiol resistance and alters metal homeostasis.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Conservation of key elements of natural competence in Lactococcus lactis ssp.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

Characterization of AcmB, an N-acetylglucosaminidase autolysin from Lactococcus lactis

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3472324

SpxB RegulatesO-Acetylation-dependent Resistance ofLactococcus lactisPeptidoglycan to Hydrolysis

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22747501

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-13-299

1 reference

Dimensions Publication ID

1 August 2017

0 references

1 reference

1 August 2017

1 reference