PreOpDB

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PreOpDB

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

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preopdb

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

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Other names: preopdb

The Prokaryotic Operon DataBase constitutes one of the most precise and complete repositories of operon predictions now available. Using our novel and highly accurate operon identification algorithm, we have predicted the operon structures of more than 1200 prokaryotic genomes. ProOpDB offers diverse alternatives by which a set of operon predictions can be retrieved.

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Publications

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ProOpDB: Prokaryotic Operon DataBase
PMID: 22096236

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

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• ProOpDB: Prokaryotic Operon DataBase PubMed citations: 97.

  97 articles citing: ProOpDB: Prokaryotic Operon DataBase

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  Regulator of Actin-Based Motility (RoaM) Downregulates Actin Tail Formation by Rickettsia rickettsii and Is Negatively Selected in Mammalian Cell Culture. PMID:35285700

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  Expression of the AHPND Toxins PirAvp and PirBvp Is Regulated by Components of the Vibrio parahaemolyticus Quorum Sensing (QS) System. PMID:35270031

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  OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data. PMID:34986143

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  Predicting Selective RNA Processing and Stabilization Operons in Clostridium spp. PMID:34177856

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  Identification of a Novel Class of Photolyases as Possible Ancestors of Their Family. PMID:34175934

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  Carbohydrate-controlled serine protease inhibitor (serpin) production in Bifidobacterium longum subsp. longum. PMID:33790385

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  A Burkholderia thailandensis DedA Family Membrane Protein Is Required for Proton Motive Force Dependent Lipid A Modification. PMID:33510730

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  Detecting operons in bacterial genomes via visual representation learning. PMID:33483546

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  Protein dosage of the lldPRD operon is correlated with RNase E-dependent mRNA processing. PMID:33361194

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  Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea. PMID:33329479

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  Integrated Co-functional Network Analysis on the Resistance and Virulence Features in Acinetobacter baumannii. PMID:33224132

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  Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes. PMID:33125079

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  Expression of an Extracellular Protein (SMU.63) Is Regulated by SprV in Streptococcus mutans. PMID:32978138

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  Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803. PMID:32793165

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  Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing. PMID:32451472

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  Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni. PMID:32366649

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  Proteomic Changes of Klebsiella pneumoniae in Response to Colistin Treatment and crrB Mutation-Mediated Colistin Resistance. PMID:32229491

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  Basal-Level Effects of (p)ppGpp in the Absence of Branched-Chain Amino Acids in Actinobacillus pleuropneumoniae. PMID:32015147

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  General and Genomic DNA-Binding Specificity for the Thermus thermophilus HB8 Transcription Factor TTHB023. PMID:31935968

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  Towards Exploring Toxin-Antitoxin Systems in Geobacillus: A Screen for Type II Toxin-Antitoxin System Families in a Thermophilic Genus. PMID:31771094

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  Bioinformatic Analysis of the Type VI Secretion System and Its Potential Toxins in the Acinetobacter Genus. PMID:31736933

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  A multi-scale coevolutionary approach to predict interactions between protein domains. PMID:31634362

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  Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts. PMID:31611373

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  Identification and Characterization of Preferred DNA-Binding Sites for the Thermus thermophilus HB8 Transcriptional Regulator TTHA0973. PMID:31284644

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  rSeqTU-A Machine-Learning Based R Package for Prediction of Bacterial Transcription Units. PMID:31156694

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  A computational system for identifying operons based on RNA-seq data. PMID:30953757

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  Prediction and large-scale analysis of primary operons in plastids reveals unique genetic features in the evolution of chloroplasts. PMID:30828719

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  Identification, Functional Characterization, and Regulon Prediction of the Zinc Uptake Regulator (zur) of Bacillus anthracis - An Insight Into the Zinc Homeostasis of the Pathogen. PMID:30687290

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  Relation of the pdxB-usg-truA-dedA Operon and the truA Gene to the Intracellular Survival of Salmonella enterica Serovar Typhimurium. PMID:30658401

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  Changes in Transcriptome of Yersinia pseudotuberculosis IP32953 Grown at 3 and 28°C Detected by RNA Sequencing Shed Light on Cold Adaptation. PMID:30538955

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  In vivo 3'-to-5' exoribonuclease targetomes of Streptococcus pyogenes. PMID:30381461

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  Metabolic adaptations underlying genome flexibility in prokaryotes. PMID:30372443

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  Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638. PMID:30248960

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  Functional Characterization of c-di-GMP Signaling-Related Genes in the Probiotic Lactobacillus acidophilus. PMID:30210464

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  SLING: a tool to search for linked genes in bacterial datasets. PMID:30124998

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  Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes. PMID:29931111

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  Genome-wide screening of potential RNase Y-processed mRNAs in the M49 serotype Streptococcus pyogenes NZ131. PMID:29900693

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  Parallels between experimental and natural evolution of legume symbionts. PMID:29891837

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  Genes Activated by Vibrio cholerae upon Exposure to Caenorhabditis elegans Reveal the Mannose-Sensitive Hemagglutinin To Be Essential for Colonization. PMID:29794057

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  Comparison of Alicyclobacillus acidocaldarius o-Succinylbenzoate Synthase to Its Promiscuous N-Succinylamino Acid Racemase/ o-Succinylbenzoate Synthase Relatives. PMID:29767960

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  Design Strategy of Multi-electron Transfer Catalysts Based on a Bioinformatic Analysis of Oxygen Evolution and Reduction Enzymes. PMID:29756682

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  Two dd-Carboxypeptidases from Mycobacterium smegmatis Affect Cell Surface Properties through Regulation of Peptidoglycan Cross-Linking and Glycopeptidolipids. PMID:29735762

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  Formation of chimeric genes with essential functions at the origin of eukaryotes. PMID:29534719

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  Identification and characterization of preferred DNA-binding sites for the Thermus thermophilus transcriptional regulator FadR. PMID:28902898

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  Comparative genomics and phylogenomic analyses of lysine riboswitch distributions in bacteria. PMID:28873470

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  MCE domain proteins: conserved inner membrane lipid-binding proteins required for outer membrane homeostasis. PMID:28819315

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  Outer membrane phospholipase A's roles in Helicobacter pylori acid adaptation. PMID:28616083

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  The Type IX Secretion System (T9SS): Highlights and Recent Insights into Its Structure and Function. PMID:28603700

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  [Expression, purification and activity analysis of GGDEF and EAL domain-containing proteins from Lactobacillus acidophilus]. PMID:28539286

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  Transcriptional Control of the Lateral-Flagellar Genes of Bradyrhizobium diazoefficiens. PMID:28533217

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  Effect of genomic distance on coexpression of coregulated genes in E. coli. PMID:28419102

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  Differential regulation of riboflavin supply genes in Vibrio cholerae. PMID:28239422

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  Analysis of Spo0M function in Bacillus subtilis. PMID:28234965

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  Non-ribosomal peptide synthetases: Identifying the cryptic gene clusters and decoding the natural product. PMID:28229977

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  Pleiotropic Regulation of Virulence Genes in Streptococcus mutans by the Conserved Small Protein SprV. PMID:28167518

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  Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans. PMID:27852217

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  Xenobiotic-metabolizing enzymes in Bacillus anthracis: molecular and functional analysis of a truncated arylamine N-acetyltransferase isozyme. PMID:27846346

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  Widespread formation of alternative 3' UTR isoforms via transcription termination in archaea. PMID:27670118

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  The Secreted Protease PrtA Controls Cell Growth, Biofilm Formation and Pathogenicity in Xylella fastidiosa. PMID:27492542

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  A novel intrinsically disordered outer membrane lipoprotein of Aggregatibacter actinomycetemcomitans binds various cytokines and plays a role in biofilm response to interleukin-1β and interleukin-8. PMID:27459270

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  Identification of Preferred DNA-Binding Sites for the Thermus thermophilus Transcriptional Regulator SbtR by the Combinatorial Approach REPSA. PMID:27428627

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  Investigating Evolutionary Dynamics of RHA1 Operons. PMID:27398020

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  Tolerance to oxidative stress is required for maximal xylem colonization by the xylem-limited bacterial phytopathogen, Xylella fastidiosa. PMID:27377476

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  Conserved Units of Co-Expression in Bacterial Genomes: An Evolutionary Insight into Transcriptional Regulation. PMID:27195891

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  Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation. PMID:27107716

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  Different Transcriptional Responses from Slow and Fast Growth Rate Strains of Listeria monocytogenes Adapted to Low Temperature. PMID:26973610

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  Systematic Mutational Analysis of Histidine Kinase Genes in the Nosocomial Pathogen Stenotrophomonas maltophilia Identifies BfmAK System Control of Biofilm Development. PMID:26873318

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  Using host-pathogen protein interactions to identify and characterize Francisella tularensis virulence factors. PMID:26714771

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  Characterization of New Virulence Factors Involved in the Intracellular Growth and Survival of Burkholderia pseudomallei. PMID:26712202

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  Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach. PMID:26677108

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  OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes. PMID:26543854

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  Carboxydotrophic growth of Geobacter sulfurreducens. PMID:26481622

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  Enhanced biofilm formation and multi-host transmission evolve from divergent genetic backgrounds in Campylobacter jejuni. PMID:26373338

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  The conserved carboxyl domain of MorC, an inner membrane protein of Aggregatibacter actinomycetemcomitans, is essential for membrane function. PMID:26205976

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  The diversity of membrane transporters encoded in bacterial arsenic-resistance operons. PMID:26020003

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  Databases for Microbiologists. PMID:26013493

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  Secondary structural entropy in RNA switch (Riboswitch) identification. PMID:25928324

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  Proteomic Investigation of the Response of Enterococcus faecalis V583 when Cultivated in Urine. PMID:25915650

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  Co-regulation of translation in protein complexes. PMID:25909184

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  σ54-Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111. PMID:25841012

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  A cluster of four homologous small RNAs modulates C1 metabolism and the pyruvate dehydrogenase complex in Rhodobacter sphaeroides under various stress conditions. PMID:25777678

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  Plasmids are vectors for redundant chromosomal genes in the Bacillus cereus group. PMID:25608745

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  Pyrococcus furiosus flagella: biochemical and transcriptional analyses identify the newly detected flaB0 gene to encode the major flagellin. PMID:25566211

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  The Vibrio cholerae VprA-VprB two-component system controls virulence through endotoxin modification. PMID:25538196

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  Computational and experimental analysis of the secretome of Methylococcus capsulatus (Bath). PMID:25479164

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  Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium. PMID:25361977

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  MetaProx: the database of metagenomic proximons. PMID:25288655

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  Genome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis. PMID:25233219

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  The coding and noncoding architecture of the Caulobacter crescentus genome. PMID:25078267

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  Elucidation of operon structures across closely related bacterial genomes. PMID:24959722

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  The transcriptome landscape of Prochlorococcus MED4 and the factors for stabilizing the core genome. PMID:24438106

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  The multifunctional role of the pallilysin-associated Treponema pallidum protein, Tp0750, in promoting fibrinolysis and extracellular matrix component degradation. PMID:24303899

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  Linkage, mobility, and selfishness in the MazF family of bacterial toxins: a snapshot of bacterial evolution. PMID:24265503

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  DOOR 2.0: presenting operons and their functions through dynamic and integrated views. PMID:24214966

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  Natural selection for operons depends on genome size. PMID:24201372

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  Measurements of mRNA degradation in Borrelia burgdorferi. PMID:23974029

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  Evidence classification of high-throughput protocols and confidence integration in RegulonDB. PMID:23327937

Tags:

Tags

More detailed information about this field from each metasource. ×

gene structure

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

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endocrinology and metabolism

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

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molecular interactions, pathways and networks

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

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model organisms

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

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phylogenetics

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:20.083989

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gene structure endocrinology and metabolism molecular interactions, pathways and networks model organisms phylogenetics