Phylogenetic Co-Occurrence of ExoR, ExoS, and ChvI, Components of the RSI Bacterial Invasion Switch, Suggests a Key Adaptive Mechanism Regulating the Transition between Free-Living and Host-Invading Phases in Rhizobiales

Agrobacterium tumefaciens ExoR Controls Acid Response Genes and Impacts Exopolysaccharide Synthesis, Horizontal Gene Transfer, and Virulence Gene Expression

(2014) B. C. Heckel et al.   JOURNAL OF BACTERIOLOGY

Molecular modeling and computational analyses suggests that theSinorhizobium melilotiperiplasmic regulator protein ExoR adopts a superhelical fold and is controlled by a unique mechanism of proteolysis

(2014) Eliza M. Wiech et al.   PROTEIN SCIENCE

Members of the Sinorhizobium meliloti ChvI regulon identified by a DNA binding screen

(2013) Louise Bélanger et al.   BMC MICROBIOLOGY

Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups

(2013) Dongying Wu et al.   PLoS One

Genome of the marine alphaproteobacterium Hoeflea phototrophica type strain (DFL-43T)

(2013) Anne Fiebig et al.   Standards in Genomic Sciences

Discriminative modelling of context-specific amino acid substitution probabilities

(2012) Christof Angermüller et al.   BIOINFORMATICS

The inner membrane histidine kinase EnvZ senses osmolality via helix-coil transitions in the cytoplasm

(2012) Loo Chien Wang et al.   EMBO JOURNAL

Sinorhizobium meliloti ExoR Is the Target of Periplasmic Proteolysis

(2012) H.-Y. Lu et al.   JOURNAL OF BACTERIOLOGY

CDD: conserved domains and protein three-dimensional structure

(2012) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Acid-Induced Type VI Secretion System Is Regulated by ExoR-ChvG/ChvI Signaling Cascade in Agrobacterium tumefaciens

(2012) Chih-Feng Wu et al.   PLoS Pathogens

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates

(2011) Y. Yang et al.   BIOINFORMATICS

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

SMART 7: recent updates to the protein domain annotation resource

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

(2011) P. Di Tommaso et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

The BatR/BatS Two-Component Regulatory System Controls the Adaptive Response of Bartonella henselae during Human Endothelial Cell Infection

(2010) M. Quebatte et al.   JOURNAL OF BACTERIOLOGY

Agrobacterium tumefaciens ExoR represses succinoglycan biosynthesis and is required for biofilm formation and motility

(2010) A. D. Tomlinson et al.   MICROBIOLOGY-SGM

Autoregulation of Sinorhizobium meliloti exoR gene expression

(2010) H.-Y. Lu et al.   MICROBIOLOGY-SGM

The Cpx envelope stress response both facilitates and inhibits elaboration of the enteropathogenic Escherichia coli bundle-forming pilus

(2010) Stefanie L. Vogt et al.   MOLECULAR MICROBIOLOGY

Sinorhizobium meliloti1021 Loss-of-Function Deletion Mutation inchvIand Its Phenotypic Characteristics

(2010) Chunxia Wang et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

GenBank

(2010) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Analysis of the Brucella abortus BvrR/BvrS Two-Component Regulatory System

(2010) Cristina Viadas et al.   PLoS One

The three-component signalling system HbpS–SenS–SenR as an example of a redox sensing pathway in bacteria

(2009) Darío Ortiz de Orué Lucana et al.   AMINO ACIDS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination

(2009) Anna Lobley et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Characterization of a Gene Family of Outer Membrane Proteins (ropB) in Rhizobium leguminosarum bv. viciae VF39SM and the Role of the Sensor Kinase ChvG in Their Regulation

(2009) D. L. Foreman et al.   JOURNAL OF BACTERIOLOGY

Identification of Direct Transcriptional Target Genes of ExoS/ChvI Two-Component Signaling in Sinorhizobium meliloti

(2009) E. J. Chen et al.   JOURNAL OF BACTERIOLOGY

Whole-Genome-Based Phylogeny and Divergence of the Genus Brucella

(2009) J. T. Foster et al.   JOURNAL OF BACTERIOLOGY

Null mutations inSinorhizobium meliloti exoSandchvIdemonstrate the importance of this two-component regulatory system for symbiosis

(2009) Louise Bélanger et al.   MOLECULAR MICROBIOLOGY

Sequence context-specific profiles for homology searching

(2009) A. Biegert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Building and assessing atomic models of proteins from structural templates: Learning and benchmarks

(2009) Brinda Kizhakke Vallat et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Molecular Determinants of a Symbiotic Chronic Infection

(2008) Katherine E. Gibson et al.   Annual Review of Genetics

Coordinating Nodule Morphogenesis with Rhizobial Infection in Legumes

(2008) Giles E.D. Oldroyd et al.   Annual Review of Plant Biology

OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar

(2008) Håkan Viklund et al.   BIOINFORMATICS

The periplasmic regulator ExoR inhibits ExoS/ChvI two-component signalling inSinorhizobium meliloti

(2008) Esther J. Chen et al.   MOLECULAR MICROBIOLOGY

Sinorhizobium melilotiRegulator MucR Couples Exopolysaccharide Synthesis and Motility

(2008) Christelle Bahlawane et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins

(2008) Brinda Kizhakke Vallat et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY