Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics

Efficient Sulfide Assimilation in Methanosarcina acetivorans Is Mediated by the MA1715 Protein

(2016) Benjamin Julius Rauch et al.   JOURNAL OF BACTERIOLOGY

Homocysteine Is Biosynthesized from Aspartate Semialdehyde and Hydrogen Sulfide in Methanogenic Archaea

(2015) Kylie D. Allen et al.   BIOCHEMISTRY

The essential gene set of a photosynthetic organism

(2015) Benjamin E. Rubin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons

(2015) Kelly M. Wetmore et al.   mBio

Harnessing the landscape of microbial culture media to predict new organism–media pairings

(2015) Matthew A. Oberhardt et al.   Nature Communications

LESS IS MORE: SELECTIVE ADVANTAGES CAN EXPLAIN THE PREVALENT LOSS OF BIOSYNTHETIC GENES IN BACTERIA

(2014) Glen D'Souza et al.   EVOLUTION

The redundant aminotransferases in lysine and arginine synthesis and the extent of aminotransferase redundancy inEscherichia coli

(2014) Piyush Behari Lal et al.   MOLECULAR MICROBIOLOGY

Novel proteins for homocysteine biosynthesis in anaerobic microorganisms

(2014) Benjamin Julius Rauch et al.   MOLECULAR MICROBIOLOGY

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Syntrophic exchange in synthetic microbial communities

(2014) M. T. Mee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Genomics with a Comprehensive Library of Transposon Mutants for the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20

(2014) J. V. Kuehl et al.   mBio

The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20

(2014) Morgan N. Price et al.   Frontiers in Microbiology

Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway

(2014) Valérie de Crécy-Lagard   Computational and Structural Biotechnology Journal

Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria

(2013) Samay Pande et al.   ISME Journal

Alternative Pyrimidine Biosynthesis Protein ApbE Is a Flavin Transferase Catalyzing Covalent Attachment of FMN to a Threonine Residue in Bacterial Flavoproteins

(2013) Yulia V. Bertsova et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Improving Microbial Genome Annotations in an Integrated Database Context

(2013) I-Min A. Chen et al.   PLoS One

Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life

(2012) Sebastian Thole et al.   ISME Journal

Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium

(2012) Paul Carini et al.   ISME Journal

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions

(2011) Adam Deutschbauer et al.   PLoS Genetics

Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments

(2011) Florence Wisniewski-Dyé et al.   PLoS Genetics

Genetics and Regulation of the Major Enzymes of Alanine Synthesis in Escherichia coli

(2010) S. H. Kim et al.   JOURNAL OF BACTERIOLOGY

Protein Thiocarboxylate-Dependent Methionine Biosynthesis inWolinella succinogenes

(2010) Kalyanaraman Krishnamoorthy et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A universal TagModule collection for parallel genetic analysis of microorganisms

(2010) Julia Oh et al.   NUCLEIC ACIDS RESEARCH

Development of a Markerless Genetic Exchange System for Desulfovibrio vulgaris Hildenborough and Its Use in Generating a Strain with Increased Transformation Efficiency

(2009) K. L. Keller et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

MicrobesOnline: an integrated portal for comparative and functional genomics

(2009) P. S. Dehal et al.   NUCLEIC ACIDS RESEARCH

RamA, a Protein Required for Reductive Activation of Corrinoid-dependent Methylamine Methyltransferase Reactions in Methanogenic Archaea

(2008) Tsuneo Ferguson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

From one amino acid to another: tRNA-dependent amino acid biosynthesis

(2008) K. Sheppard et al.   NUCLEIC ACIDS RESEARCH