FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies
Authors
Keywords
-
Journal
Frontiers in Microbiology
Volume 11, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2020-01-31
DOI
10.3389/fmicb.2020.00037
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers
- (2019) Fengbin Wang et al. CELL
- TonB-Dependent Receptor Repertoire of Pseudomonas aeruginosa for Uptake of Siderophore-Drug Conjugates
- (2018) Alexandre Luscher et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- MAPLE 2.3.0: an improved system for evaluating the functionomes of genomes and metagenomes
- (2018) Wataru Arai et al. BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
- Ironing out siderophore biosynthesis: a review of non-ribosomal peptide synthetase (NRPS)-independent siderophore synthetases
- (2018) Cassandra S. Carroll et al. CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY
- Expression of Novel Gene Content Drives Adaptation to Low Iron in the Cyanobacterium Acaryochloris
- (2018) Amy L Gallagher et al. Genome Biology and Evolution
- The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans
- (2018) Benjamin J. Tully et al. Scientific Data
- Multi-heme cytochromes provide a pathway for survival in energy-limited environments
- (2018) Xiao Deng et al. Science Advances
- A flavin-based extracellular electron transfer mechanism in diverse Gram-positive bacteria
- (2018) Samuel H. Light et al. NATURE
- In situ electrochemical enrichment and isolation of a magnetite-reducing bacterium from a high pH serpentinizing spring
- (2017) Annette R. Rowe et al. ENVIRONMENTAL MICROBIOLOGY
- Expression patterns of elemental cycling genes in the Amazon River Plume
- (2017) Brandon M Satinsky et al. ISME Journal
- Hidden diversity revealed by genome-resolved metagenomics of iron-oxidizing microbial mats from Lō’ihi Seamount, Hawai’i
- (2017) Heather Fullerton et al. ISME Journal
- Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars
- (2017) Shino Suzuki et al. ISME Journal
- Nonribosomal peptide synthetase biosynthetic clusters of ESKAPE pathogens
- (2017) Andrew M. Gulick NATURAL PRODUCT REPORTS
- MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
- (2017) Martin Steinegger et al. NATURE BIOTECHNOLOGY
- Comparative Genomic Analysis of Neutrophilic Iron(II) Oxidizer Genomes for Candidate Genes in Extracellular Electron Transfer
- (2017) Shaomei He et al. Frontiers in Microbiology
- Novel Pelagic Iron-Oxidizing Zetaproteobacteria from the Chesapeake Bay Oxic–Anoxic Transition Zone
- (2017) Beverly K. Chiu et al. Frontiers in Microbiology
- In vitro heme biotransformation by the HupZ enzyme from Group A streptococcus
- (2016) Ankita J. Sachla et al. BIOMETALS
- Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer
- (2016) Talia N M Jewell et al. ISME Journal
- BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences
- (2016) Minoru Kanehisa et al. JOURNAL OF MOLECULAR BIOLOGY
- Magnetosome biogenesis in magnetotactic bacteria
- (2016) René Uebe et al. NATURE REVIEWS MICROBIOLOGY
- UniProt: the universal protein knowledgebase
- (2016) NUCLEIC ACIDS RESEARCH
- Biogeography of a human oral microbiome at the micron scale
- (2016) Jessica L. Mark Welch et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
- (2016) Karthik Anantharaman et al. Nature Communications
- The Irony of Iron – Biogenic Iron Oxides as an Iron Source to the Ocean
- (2016) David Emerson Frontiers in Microbiology
- Regulation of Pseudomonas aeruginosa Virulence by Distinct Iron Sources
- (2016) Alexandria Reinhart et al. Genes
- A new view of the tree of life
- (2016) Laura A. Hug et al. Nature Microbiology
- A Ferrous Iron Exporter Mediates Iron Resistance in Shewanella oneidensis MR-1
- (2015) Brittany D. Bennett et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- New Insight into Microbial Iron Oxidation as Revealed by the Proteomic Profile of an Obligate Iron-Oxidizing Chemolithoautotroph
- (2015) Roman A. Barco et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- The aerobic respiratory chain of the acidophilic archaeon Ferroplasma acidiphilum : A membrane-bound complex oxidizing ferrous iron
- (2015) Cindy J. Castelle et al. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
- Diving into the redox properties of Geobacter sulfurreducens cytochromes: a model for extracellular electron transfer
- (2015) Telma C. Santos et al. DALTON TRANSACTIONS
- Single-cell genomics of uncultivated deep-branching magnetotactic bacteria reveals a conserved set of magnetosome genes
- (2015) Sebastian Kolinko et al. ENVIRONMENTAL MICROBIOLOGY
- An update on iron acquisition by Legionella pneumophila: new pathways for siderophore uptake and ferric iron reduction
- (2015) Nicholas P Cianciotto Future Microbiology
- Unusual biology across a group comprising more than 15% of domain Bacteria
- (2015) Christopher T. Brown et al. NATURE
- antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
- (2015) Tilmann Weber et al. NUCLEIC ACIDS RESEARCH
- The Pfam protein families database: towards a more sustainable future
- (2015) Robert D. Finn et al. NUCLEIC ACIDS RESEARCH
- Feasible metabolisms in high pH springs of the Philippines
- (2015) Dawn Cardace et al. Frontiers in Microbiology
- The FUR (ferric uptake regulator) superfamily: Diversity and versatility of key transcriptional regulators
- (2014) María F. Fillat ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
- Trimmomatic: a flexible trimmer for Illumina sequence data
- (2014) Anthony M. Bolger et al. BIOINFORMATICS
- Heme uptake in bacterial pathogens
- (2014) Heidi Contreras et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- Crystallographic and Spectroscopic Insights into Heme Degradation by Mycobacterium tuberculosis MhuD
- (2014) Amanda B. Graves et al. INORGANIC CHEMISTRY
- An environmental bacterial taxon with a large and distinct metabolic repertoire
- (2014) Micheal C. Wilson et al. NATURE
- Unraveling the Stratification of an Iron-Oxidizing Microbial Mat by Metatranscriptomics
- (2014) Achim Quaiser et al. PLoS One
- Molecular and Evolutionary Analysis of NEAr-Iron Transporter (NEAT) Domains
- (2014) Erin S. Honsa et al. PLoS One
- Genomic analyses of bacterial porin-cytochrome gene clusters
- (2014) Liang Shi et al. Frontiers in Microbiology
- Molecular characterization of vulnibactin biosynthesis in Vibrio vulnificus indicates the existence of an alternative siderophore
- (2014) Wenzhi Tan et al. Frontiers in Microbiology
- Structural and functional characterization of an Isd-type haem-degradation enzyme fromListeria monocytogenes
- (2014) Thao Duong et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
- Heme oxygenation and the widening paradigm of heme degradation
- (2013) Angela Wilks et al. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
- The Bacillus subtilis EfeUOB transporter is essential for high-affinity acquisition of ferrous and ferric iron
- (2013) Marcus Miethke et al. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
- Collaborative microbial Fe-redox cycling by pelagic floc bacteria across wide ranging oxygenated aquatic systems
- (2013) A.V.C. Elliott et al. CHEMICAL GEOLOGY
- Coordinated transporter activity shapes high-affinity iron acquisition in cyanobacteria
- (2013) Chana Kranzler et al. ISME Journal
- The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
- (2013) Ross Overbeek et al. NUCLEIC ACIDS RESEARCH
- Shared and distinct mechanisms of iron acquisition by bacterial and fungal pathogens of humans
- (2013) Mélissa Caza et al. Frontiers in Cellular and Infection Microbiology
- Pseudomonas aeruginosa adapts its iron uptake strategies in function of the type of infections
- (2013) Pierre Cornelis et al. Frontiers in Cellular and Infection Microbiology
- Transcriptional regulation by Ferric Uptake Regulator (Fur) in pathogenic bacteria
- (2013) Bryan Troxell et al. Frontiers in Cellular and Infection Microbiology
- Comparative genomics of freshwater Fe-oxidizing bacteria: implications for physiology, ecology, and systematics
- (2013) David Emerson et al. Frontiers in Microbiology
- An ABC Transporter with Two Periplasmic Binding Proteins Involved in Iron Acquisition in Pseudomonas aeruginosa
- (2012) Karl Brillet et al. ACS Chemical Biology
- Insight into the evolution of the iron oxidation pathways
- (2012) Marianne Ilbert et al. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
- Bacillus subtilis HmoB is a heme oxygenase with a novel structure
- (2012) Seong-Hun Park et al. BMB Reports
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- (2012) Anton Bankevich et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- A novel iron- and copper-binding protein in the Lyme disease spirochaete
- (2012) Peng Wang et al. MOLECULAR MICROBIOLOGY
- Multiple ABC transporters are involved in the acquisition of petrobactin inBacillus anthracis
- (2012) Shandee D. Dixon et al. MOLECULAR MICROBIOLOGY
- The ‘porin-cytochrome’ model for microbe-to-mineral electron transfer
- (2012) David J. Richardson et al. MOLECULAR MICROBIOLOGY
- Analysis of the Global Ocean Sampling (GOS) Project for Trends in Iron Uptake by Surface Ocean Microbes
- (2012) Eve Toulza et al. PLoS One
- Surface multiheme c-type cytochromes from Thermincola potens and implications for respiratory metal reduction by Gram-positive bacteria
- (2012) H. K. Carlson et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Crystal structure of HutZ, a heme storage protein from Vibrio cholerae: A structural mismatch observed in the region of high sequence conservation
- (2012) Xiuhua Liu et al. BMC STRUCTURAL BIOLOGY
- Identification and Characterization of MtoA: A Decaheme c-Type Cytochrome of the Neutrophilic Fe(II)-Oxidizing Bacterium Sideroxydans lithotrophicus ES-1
- (2012) Juan Liu et al. Frontiers in Microbiology
- Crystal structure of Campylobacter jejuni ChuZ: A split-barrel family heme oxygenase with a novel heme-binding mode
- (2011) Rui Zhang et al. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
- TonB or not TonB: is that the question?This paper is one of a selection of papers published in a Special Issue entitled CSBMCB 53rd Annual Meeting — Membrane Proteins in Health and Disease, and has undergone the Journal’s usual peer review process.
- (2011) Karla D. Krewulak et al. Biochemistry and Cell Biology
- The Siderophore Binding Protein FeuA Shows Limited Promiscuity toward Exogenous Triscatecholates
- (2011) Florian Peuckert et al. CHEMISTRY & BIOLOGY
- Dynamics of Gene Duplication in the Genomes of Chlorophyll d-Producing Cyanobacteria: Implications for the Ecological Niche
- (2011) Scott R. Miller et al. Genome Biology and Evolution
- Discovery and characterization of a unique mycobacterial heme acquisition system
- (2011) M. V. Tullius et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Prodigal: prokaryotic gene recognition and translation initiation site identification
- (2010) Doug Hyatt et al. BMC BIOINFORMATICS
- Hidden Markov model speed heuristic and iterative HMM search procedure
- (2010) L Steven Johnson et al. BMC BIOINFORMATICS
- Crystal Structure of HugZ, a Novel Heme Oxygenase fromHelicobacter pylori
- (2010) Yonglin Hu et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- The IsdG-family of haem oxygenases degrades haem to a novel chromophore
- (2010) Michelle L. Reniere et al. MOLECULAR MICROBIOLOGY
- A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria
- (2010) S. Lucker et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Characterization of Prochlorococcus clades from iron-depleted oceanic regions
- (2010) D. B. Rusch et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Recent advances in siderophore biosynthesis
- (2009) Sarah M Barry et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- Potential for Iron-reduction and Iron-cycling in Iron Oxyhydroxide-rich Microbial Mats at Loihi Seamount
- (2009) David Emerson GEOMICROBIOLOGY JOURNAL
- Bacterial competition: surviving and thriving in the microbial jungle
- (2009) Michael E. Hibbing et al. NATURE REVIEWS MICROBIOLOGY
- Anguibactin- versus vanchrobactin-mediated iron uptake in Vibrio anguillarum: evolution and ecology of a fish pathogen
- (2009) Manuel L. Lemos et al. Environmental Microbiology Reports
- Unique Structure and Stability of HmuY, a Novel Heme-Binding Protein of Porphyromonas gingivalis
- (2009) Halina Wójtowicz et al. PLoS Pathogens
- Bacterial heme-transport proteins and their heme-coordination modes
- (2008) Yong Tong et al. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
- Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community
- (2008) Chris Jeans et al. ISME Journal
- A New Iron-oxidizing/O2-reducing Supercomplex Spanning Both Inner and Outer Membranes, Isolated from the Extreme AcidophileAcidithiobacillus ferrooxidans
- (2008) Cindy Castelle et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina
- (2008) W. D. Swingley et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Signaling mechanisms for activation of extracytoplasmic function (ECF) sigma factors
- (2007) Benjamin E. Brooks et al. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now