MicrobesOnline

Names
More detailed information about this field from each metasource.

MicrobesOnline
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:01.449908

microbesonline
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:01.449908

Other names: microbesonline

A suite of Web-based tools for comparative genomics

Webpage:

http://www.MicrobesOnline.org

Publications:

Publications
More detailed information about this field from each metasource.

MicrobesOnline: an integrated portal for comparative and functional genomics
PMID: 19906701
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:01.449908

http://nar.oxfordjournals.org/content/38/suppl_1/D396
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

MicrobesOnline: an integrated portal for comparative and functional genomics PubMed citations: 251.

251 articles citing: MicrobesOnline: an integrated portal for comparative and functional genomics

Myxopyronin B inhibits growth of a Fidaxomicin-resistant Clostridioides difficile isolate and interferes with toxin synthesis. PMID:34991700
OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data. PMID:34986143
Predictive regulatory and metabolic network models for systems analysis of Clostridioides difficile. PMID:34637780
Large-scale identification of extracellular plant miRNAs in mammals implicates their dietary intake. PMID:34587184
Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase. PMID:34572495
Comparative Analysis of the IclR-Family of Bacterial Transcription Factors and Their DNA-Binding Motifs: Structure, Positioning, Co-Evolution, Regulon Content. PMID:34177859
Mycobacterial Populations Partly Change the Proportions of the Cells Undergoing Asymmetric/Symmetric Divisions in Response to Glycerol Levels in Growth Medium. PMID:34064643
A comprehensive review of m6A/m6Am RNA methyltransferase structures. PMID:34023900
The Phosin PptA Plays a Negative Role in the Regulation of Antibiotic Production in Streptomyces lividans. PMID:33804592
Deletion Mutants, Archived Transposon Library, and Tagged Protein Constructs of the Model Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough. PMID:33737356
Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments. PMID:33657378
Four families of folate-independent methionine synthases. PMID:33534785
BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence. PMID:33532841
In Silico Characterization of Toxin-Antitoxin Systems in Campylobacter Isolates Recovered from Food Sources and Sporadic Human Illness. PMID:33430508
Microbial Musings - October 2020. PMID:33124974
Prometheus, an omics portal for interkingdom comparative genomic analyses. PMID:33112870
Hemoglobin stimulates vigorous growth of Streptococcus pneumoniae and shapes the pathogen's global transcriptome. PMID:32938947
Redefining the Clostridioides difficile σB Regulon: σB Activates Genes Involved in Detoxifying Radicals That Can Result from the Exposure to Antimicrobials and Hydrogen Peroxide. PMID:32938698
The Salmonella enterica serovar Typhimurium virulence factor STM3169 is a hexuronic acid binding protein component of a TRAP transporter. PMID:32894213
Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature. PMID:32817099
Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4. PMID:32804944
Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum. PMID:32723790
GapMind: Automated Annotation of Amino Acid Biosynthesis. PMID:32576650
Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks. PMID:32487739
Revisiting the expression signature of pks15/1 unveils regulatory patterns controlling phenolphtiocerol and phenolglycolipid production in pathogenic mycobacteria. PMID:32379829
An Integrated Multi-Disciplinary Perspectivefor Addressing Challenges of the Human Gut Microbiome. PMID:32155792
Changes in the expression of genes encoding type IV pili-associated proteins are seen when Clostridium perfringens is grown in liquid or on surfaces. PMID:31937237
Characterization of FliL Proteins in Bradyrhizobium diazoefficiens: Lateral FliL Supports Swimming Motility, and Subpolar FliL Modulates the Lateral Flagellar System. PMID:31843800
Anion transport as a target of adaption to perchlorate in sulfate-reducing communities. PMID:31659234
gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions. PMID:31584099
Genomic reconstruction of σ54 regulons in Clostridiales. PMID:31288763
Mr.Vc: a database of microarray and RNA-seq of Vibrio cholerae. PMID:31231774
rSeqTU-A Machine-Learning Based R Package for Prediction of Bacterial Transcription Units. PMID:31156694
Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease. PMID:31092280
The Primary Antisense Transcriptome of Halobacterium salinarum NRC-1. PMID:30959844
Curated BLAST for Genomes. PMID:30944879
Defining the regulon of genes controlled by σE , a key regulator of the cell envelope stress response in Streptomyces coelicolor. PMID:30907454
A Comparison of Microbial Genome Web Portals. PMID:30853946
Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism. PMID:30746495
Rational construction of genome-reduced and high-efficient industrial Streptomyces chassis based on multiple comparative genomic approaches. PMID:30691531
Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC. PMID:30296937
Novel Metabolic Pathways and Regulons for Hexuronate Utilization in Proteobacteria. PMID:30249705
Jungle Express is a versatile repressor system for tight transcriptional control. PMID:30190458
Complex Iron Uptake by the Putrebactin-Mediated and Feo Systems in Shewanella oneidensis. PMID:30097446
Shewanella oneidensis MR-1 Utilizes both Sodium- and Proton-Pumping NADH Dehydrogenases during Aerobic Growth. PMID:29654176
Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp. PMID:29593678
Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. PMID:29324779
Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems. PMID:29263101
Sugar Lego: gene composition of bacterial carbohydrate metabolism genomic loci. PMID:29178959
COGNAT: a web server for comparative analysis of genomic neighborhoods. PMID:29166914
Granzyme B Disrupts Central Metabolism and Protein Synthesis in Bacteria to Promote an Immune Cell Death Program. PMID:29107333
Unintended Laboratory-Driven Evolution Reveals Genetic Requirements for Biofilm Formation by Desulfovibrio vulgaris Hildenborough. PMID:29042504
A metabolic pathway for catabolizing levulinic acid in bacteria. PMID:28947739
A Quorum-Sensing System That Regulates Streptococcus pneumoniae Biofilm Formation and Surface Polysaccharide Production. PMID:28932816
Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides. PMID:28912798
Identification and Characterization of the Major Porin of Desulfovibrio vulgaris Hildenborough. PMID:28874410
PaperBLAST: Text Mining Papers for Information about Homologs. PMID:28845458
The t6A modification acts as a positive determinant for the anticodon nuclease PrrC, and is distinctively nonessential in Streptococcus mutans. PMID:28726545
DprA from Neisseria meningitidis: properties and role in natural competence for transformation. PMID:28696187
Transcriptional Control of the Lateral-Flagellar Genes of Bradyrhizobium diazoefficiens. PMID:28533217
CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline. PMID:28449639
Reconstruction of the evolution of microbial defense systems. PMID:28376755
Comparative genomics and evolution of transcriptional regulons in Proteobacteria. PMID:28348857
Comparative genomics of pyridoxal 5'-phosphate-dependent transcription factor regulons in Bacteria. PMID:28348826
Mechanism for microbial population collapse in a fluctuating resource environment. PMID:28320772
Gene expression control by Bacillus anthracis purine riboswitches. PMID:28209633
Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics. PMID:28128549
A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea. PMID:28073944
The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor. PMID:28066333
System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions. PMID:28030630
PptAB Exports Rgg Quorum-Sensing Peptides in Streptococcus. PMID:27992504
Global repositioning of transcription start sites in a plant-fermenting bacterium. PMID:27982035
A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea. PMID:27920295
Functional mining of transporters using synthetic selections. PMID:27694800
Genome sequence of Candidatus Arsenophonus lipopteni, the exclusive symbiont of a blood sucking fly Lipoptena cervi (Diptera: Hippoboscidae). PMID:27660670
Crystal Structure of the Escherichia coli Fic Toxin-Like Protein in Complex with Its Cognate Antitoxin. PMID:27657533
Functional Annotations of Paralogs: A Blessing and a Curse. PMID:27618105
Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria. PMID:27617010
Identification and Regulation of Genes for Cobalamin Transport in the Cyanobacterium Synechococcus sp. Strain PCC 7002. PMID:27457716
Complementation of Cobalamin Auxotrophy in Synechococcus sp. Strain PCC 7002 and Validation of a Putative Cobalamin Riboswitch In Vivo. PMID:27457714
Proteome analysis of the Mycobacterium tuberculosis Beijing B0/W148 cluster. PMID:27356881
Evolutionary assembly patterns of prokaryotic genomes. PMID:27197212
Comparative transcriptomics across the prokaryotic tree of life. PMID:27154273
EDGAR 2.0: an enhanced software platform for comparative gene content analyses. PMID:27098043
Comparative Proteomic Analysis of Desulfotomaculum reducens MI-1: Insights into the Metabolic Versatility of a Gram-Positive Sulfate- and Metal-Reducing Bacterium. PMID:26925055
Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis. PMID:26904004
Transcriptional Regulation of Carbohydrate Utilization Pathways in the Bifidobacterium Genus. PMID:26903998
Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported. PMID:26873250
Determination of specificity influencing residues for key transcription factor families. PMID:26753103
Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires. PMID:26752266
Gene selection and cloning approaches for co-expression and production of recombinant protein-protein complexes. PMID:26671275
Web Resources for Metagenomics Studies. PMID:26602607
Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. PMID:26565399
σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough. PMID:26555820
Two novel regulators of N-acetyl-galactosamine utilization pathway and distinct roles in bacterial infections. PMID:26540018
ATP-binding Cassette (ABC) Transport System Solute-binding Protein-guided Identification of Novel d-Altritol and Galactitol Catabolic Pathways in Agrobacterium tumefaciens C58. PMID:26472925
Reconstruction of novel transcription factor regulons through inference of their binding sites. PMID:26388177
New insights into the biological role of the osmoregulated periplasmic glucans in pathogenic and symbiotic bacteria. PMID:26265506
Biosynthesis of Squalene from Farnesyl Diphosphate in Bacteria: Three Steps Catalyzed by Three Enzymes. PMID:26258173
Nitrogen Cycling Potential of a Grassland Litter Microbial Community. PMID:26231641
Genomic potential for arsenic efflux and methylation varies among global Prochlorococcus populations. PMID:26151644
CMRegNet-An interspecies reference database for corynebacterial and mycobacterial regulatory networks. PMID:26062809
Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism. PMID:26037461
Proteins Related to the Type I Secretion System Are Associated with Secondary SecA_DEAD Domain Proteins in Some Species of Planctomycetes, Verrucomicrobia, Proteobacteria, Nitrospirae and Chlorobi. PMID:26030905
Temporal hierarchy of gene expression mediated by transcription factor binding affinity and activation dynamics. PMID:26015501
Databases for Microbiologists. PMID:26013493
Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation. PMID:25982966
Cell Cycle Control by the Master Regulator CtrA in Sinorhizobium meliloti. PMID:25978424
Novel Transcriptional Regulons for Autotrophic Cycle Genes in Crenarchaeota. PMID:25939834
CceR and AkgR regulate central carbon and energy metabolism in alphaproteobacteria. PMID:25650399
Estimation of prokaryotic supergenome size and composition from gene frequency distributions. PMID:25572821
Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota. PMID:25538694
Internal sense of direction: sensing and signaling from cytoplasmic chemoreceptors. PMID:25428939
Comparative genomics of transcriptional regulation of methionine metabolism in Proteobacteria. PMID:25411846
Comparative genomics of DtxR family regulons for metal homeostasis in Archaea. PMID:25404694
MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data. PMID:25398900
Evolution of context dependent regulation by expansion of feast/famine regulatory proteins. PMID:25394904
A high-resolution network model for global gene regulation in Mycobacterium tuberculosis. PMID:25232098
Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway. PMID:25210598
A functional genomics catalogue of activated transcription factors during pathogenesis of pneumococcal disease. PMID:25196724
A nutrient-tunable bistable switch controls motility in Salmonella enterica serovar Typhimurium. PMID:25161191
Identification of a cyclic-di-GMP-modulating response regulator that impacts biofilm formation in a model sulfate reducing bacterium. PMID:25120537
Towards an informative mutant phenotype for every bacterial gene. PMID:25112473
Phylogenetics and the human microbiome. PMID:25102857
Comparative secretome analysis of Streptomyces scabiei during growth in the presence or absence of potato suberin. PMID:25028574
Leveraging structure for enzyme function prediction: methods, opportunities, and challenges. PMID:24998033
Conservation of transcription start sites within genes across a bacterial genus. PMID:24987095
Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. PMID:24980702
Control of competence for DNA transformation in streptococcus suis by genetically transferable pherotypes. PMID:24968201
Comparative genomics and evolution of regulons of the LacI-family transcription factors. PMID:24966856
Porphyromonas gingivalis peptidylarginine deiminase, a key contributor in the pathogenesis of experimental periodontal disease and experimental arthritis. PMID:24959715
Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase. PMID:24938123
Oxidative stress enhances the expression of sulfur assimilation genes: preliminary insights on the Enterococcus faecalis iron-sulfur cluster machinery regulation. PMID:24936909
Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions. PMID:24865611
Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics. PMID:24782525
Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase. PMID:24742328
Diversity of the metal-transporting P1B-type ATPases. PMID:24729073
Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility. PMID:24639670
Extracellular DNA metabolism in Haloferax volcanii. PMID:24600440
Bioinformatics analysis of bacterial annexins--putative ancestral relatives of eukaryotic annexins. PMID:24454864
The transcriptome landscape of Prochlorococcus MED4 and the factors for stabilizing the core genome. PMID:24438106
Prospecting for unannotated enzymes: discovery of a 3',5'-nucleotide bisphosphate phosphatase within the amidohydrolase superfamily. PMID:24401123
Comparative genomics and functional analysis of rhamnose catabolic pathways and regulons in bacteria. PMID:24391637
Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks. PMID:24330590
INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles. PMID:24324765
The Structure-Function Linkage Database. PMID:24271399
Network portal: a database for storage, analysis and visualization of biological networks. PMID:24271392
Linkage, mobility, and selfishness in the MazF family of bacterial toxins: a snapshot of bacterial evolution. PMID:24265503
Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus. PMID:24250794
Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious. PMID:24198337
Gene expression profiling of Clostridium botulinum under heat shock stress. PMID:24195079
RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria. PMID:24175918
The Campylobacter jejuni CiaD effector protein activates MAP kinase signaling pathways and is required for the development of disease. PMID:24144181
Engineering dynamic pathway regulation using stress-response promoters. PMID:24142050
Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. PMID:24060102
Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila. PMID:24004689
Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima. PMID:23986752
Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes. PMID:23974031
New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. PMID:23913324
Hidden Markov models for evolution and comparative genomics analysis. PMID:23762278
Insights into the structure and metabolic function of microbes that shape pelagic iron-rich aggregates ("iron snow"). PMID:23645202
Glycolytic strategy as a tradeoff between energy yield and protein cost. PMID:23630264
Indirect and suboptimal control of gene expression is widespread in bacteria. PMID:23591776
RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. PMID:23547897
MGcV: the microbial genomic context viewer for comparative genome analysis. PMID:23547764
Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis. PMID:23504016
Improving microbial genome annotations in an integrated database context. PMID:23424620
Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria. PMID:23398941
JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison. PMID:23324080
Gene frequency distributions reject a neutral model of genome evolution. PMID:23315380
EfaR is a major regulator of Enterococcus faecalis manganese transporters and influences processes involved in host colonization and infection. PMID:23297382
Inference of gene regulatory networks from genome-wide knockout fitness data. PMID:23271269
Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth. PMID:23264581
Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum. PMID:23209028
MetaMicrobesOnline: phylogenomic analysis of microbial communities. PMID:23203984
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. PMID:23203876
Global analysis of mRNA stability in Mycobacterium tuberculosis. PMID:23125364
MBGD update 2013: the microbial genome database for exploring the diversity of microbial world. PMID:23118485
High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris. PMID:23098413
Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes. PMID:23086211
The inter-kingdom solo OryR regulator of Xanthomonas oryzae is important for motility. PMID:23083431
Comparative genomic analysis of Geobacter sulfurreducens KN400, a strain with enhanced capacity for extracellular electron transfer and electricity production. PMID:22967216
Uncovering the co-evolutionary network among prokaryotic genes. PMID:22962457
Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima. PMID:22925190
Burkholderia cenocepacia differential gene expression during host-pathogen interactions and adaptation to the host environment. PMID:22919581
Diversity and versatility of the Thermotoga maritima sugar kinome. PMID:22885293
The last rRNA methyltransferase of E. coli revealed: the yhiR gene encodes adenine-N6 methyltransferase specific for modification of A2030 of 23S ribosomal RNA. PMID:22847818
PePPER: a webserver for prediction of prokaryote promoter elements and regulons. PMID:22747501
Glutamine versus ammonia utilization in the NAD synthetase family. PMID:22720044
N-acetylgalactosamine utilization pathway and regulon in proteobacteria: genomic reconstruction and experimental characterization in Shewanella. PMID:22711537
RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. PMID:22700702
Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli. PMID:22694848
Identification of a general O-linked protein glycosylation system in Acinetobacter baumannii and its role in virulence and biofilm formation. PMID:22685409
Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. PMID:22638584
Computational tools for metabolic engineering. PMID:22629572
A unique regulator contributes to quorum sensing and virulence in Burkholderia cenocepacia. PMID:22624054
Translational web robots for pathogen genome analysis. PMID:22587672
Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus. PMID:22586090
How much can we learn about the function of bacterial rRNA modification by mining large-scale experimental datasets? PMID:22411911
A novel protein kinase-like domain in a selenoprotein, widespread in the tree of life. PMID:22359664
Mutations at several loci cause increased expression of ribonucleotide reductase in Escherichia coli. PMID:22247510
Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex. PMID:22210771
Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches. PMID:22201529
Ribulokinase and transcriptional regulation of arabinose metabolism in Clostridium acetobutylicum. PMID:22194461
Complete genome sequence of "Enterobacter lignolyticus" SCF1. PMID:22180812
Comparative microbial modules resource: generation and visualization of multi-species biclusters. PMID:22144874
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. PMID:22139929
Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PMID:22125499
Niche adaptation by expansion and reprogramming of general transcription factors. PMID:22108796
ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage. PMID:22102570
ProOpDB: Prokaryotic Operon DataBase. PMID:22096236
CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands. PMID:22080556
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. PMID:22070167
FungiDB: an integrated functional genomics database for fungi. PMID:22064857
High-sensitivity stable-isotope probing by a quantitative terminal restriction fragment length polymorphism protocol. PMID:22038597
Translesion-synthesis DNA polymerases participate in replication of the telomeres in Streptomyces. PMID:22006845
Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium. PMID:21992415
The transcriptional landscape of Chlamydia pneumoniae. PMID:21989159
Neisseria Base: a comparative genomics database for Neisseria meningitidis. PMID:21930505
One carbon metabolism in SAR11 pelagic marine bacteria. PMID:21886845
The RND-family transporter, HpnN, is required for hopanoid localization to the outer membrane of Rhodopseudomonas palustris TIE-1. PMID:21873238
Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis. PMID:21849503
Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. PMID:21840973
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. PMID:21810205
Absolute quantification of microbial proteomes at different states by directed mass spectrometry. PMID:21772258
Parallel evolution of transcriptome architecture during genome reorganization. PMID:21750103
Genetics and molecular biology of the electron flow for sulfate respiration in desulfovibrio. PMID:21747813
Defining reference sequences for Nocardia species by similarity and clustering analyses of 16S rRNA gene sequence data. PMID:21687706
Coevolution of ABC transporters and two-component regulatory systems as resistance modules against antimicrobial peptides in Firmicutes Bacteria. PMID:21665979
GLAMM: Genome-Linked Application for Metabolic Maps. PMID:21624891
A high resolution map of a cyanobacterial transcriptome. PMID:21612627
Shewanella oneidensis MR-1 sensory box protein involved in aerobic and anoxic growth. PMID:21602393
Comparative genomics of the dormancy regulons in mycobacteria. PMID:21602344
Transcriptome response of high- and low-light-adapted Prochlorococcus strains to changing iron availability. PMID:21562599
Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence. PMID:21531804
Housekeeping genes essential for pantothenate biosynthesis are plasmid-encoded in Rhizobium etli and Rhizobium leguminosarum. PMID:21463532
Shotgun sequencing of Yersinia enterocolitica strain W22703 (biotype 2, serotype O:9): genomic evidence for oscillation between invertebrates and mammals. PMID:21453472
Regulation and consequence of serine catabolism in Streptococcus pyogenes. PMID:21317320
Genome (re-)annotation and open-source annotation pipelines. PMID:21255336
Plasmids with a chromosome-like role in rhizobia. PMID:21217003
Coxiella burnetii transcriptional analysis reveals serendipity clusters of regulation in intracellular bacteria. PMID:21203564
ODB: a database for operon organizations, 2011 update. PMID:21051344
Common and divergent features in transcriptional control of the homologous small RNAs GlmY and GlmZ in Enterobacteriaceae. PMID:20965974
A widespread peroxiredoxin-like domain present in tumor suppression- and progression-implicated proteins. PMID:20964819
Genomics-driven reconstruction of acinetobacter NAD metabolism: insights for antibacterial target selection. PMID:20926389
Multi-species integrative biclustering. PMID:20920250
CheV: CheW-like coupling proteins at the core of the chemotaxis signaling network. PMID:20832320
Sinorhizobium meliloti requires a cobalamin-dependent ribonucleotide reductase for symbiosis with its plant host. PMID:20698752
Systems-level metabolic flux profiling elucidates a complete, bifurcated tricarboxylic acid cycle in Clostridium acetobutylicum. PMID:20622067
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. PMID:20542910
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. PMID:19965766
http://nar.oxfordjournals.org/content/38/suppl_1/D396

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genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

prokaryotic genome databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:01.449908

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:01.449908

gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:01.449908

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:01.449908

gene and protein families
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:01.449908

genomics prokaryotic genome model organisms gene expression molecular interactions, pathways and networks gene and protein families

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SOURCE

SubtiWiki

GreenPhylDB: A phylogenomic database for plant comparative genomics

Yeastract+

The UCSC Archaeal Genome Browser

KnockTF

Chlamydiae Database