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Bacteria genome databases | Annotation

The central role of Escherichia coli research in the history of molecular genetics, systems biology and synthetic biology make the data generated from E. coli important not only for this model organism, but also for bacteria in general, including…
GenBank
Dataset

GenBank

A comprehensive database that contains publicly available nucleotide sequences…

A comprehensive database that contains publicly available nucleotide sequences for over 300 000 formally described species. These sequences are obtained primarily through submissions from individual…

NCBI
Dataset

NCBI National Center for Biotechnology Information

Supplies several online resources for biological information. NCBI is a…

Supplies several online resources for biological information. NCBI is a web-based platform gathering information, tools, and functions that can be useful for researchers about biology. It offers user…

EcoCyc
Dataset

EcoCyc

A scientific database for the bacterium Escherichia coli K-12 MG1655. The…

A scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and…

Global Ocean…
Dataset

Global Ocean Microbiome

Provides global biodiversity resources for larger organismal size spectra.…

Provides global biodiversity resources for larger organismal size spectra. Global Ocean Microbiome is a gene catalogue and analysis of ocean microbes in their environmental context across three depth…

Pseudomonas…
Dataset

Pseudomonas Genome Database

Collaborates with an international panel of expert Pseudomonas researchers to…

Collaborates with an international panel of expert Pseudomonas researchers to provide high quality updates to the PAO1 genome annotation and make cutting edge genome analysis data available. The…

Gene
Dataset

Gene

Integrates gene-specific information from multiple data sources. NCBI Reference…

Integrates gene-specific information from multiple data sources. NCBI Reference Sequence (RefSeq) genomes for viruses, prokaryotes and eukaryotes are the primary foundation for Gene records in that…

CyanoBase
Dataset

CyanoBase

Provides an easy way of accessing the sequences and all-inclusive annotation…

Provides an easy way of accessing the sequences and all-inclusive annotation data on the structures of the cyanobacterial genomes. It contains cyanobacterial genomic sequences from 376 species, which…

PATRIC
Dataset

PATRIC Pathosystems Resource Integration Center

Aims to assist scientists in infectious-disease research. PATRIC is a National…

Aims to assist scientists in infectious-disease research. PATRIC is a National Institute of Health (NIH) supported bioinformatics resource center that has been built to enable comparative genomic…

Thermus…
Dataset

Thermus thermophilus

Presents the whole sequenced genome of Thermus thermophilus. T. thermophilus is…

Presents the whole sequenced genome of Thermus thermophilus. T. thermophilus is an extremely thermophilic bacterium, which grows optimally between 65 and 72 C. The type strain T. thermophilus HB8 was…

Flavobacterium…
Dataset

Flavobacterium psychrophilum

Presents the whole sequenced genome of Flavobacterium psychrophilum.…

Presents the whole sequenced genome of Flavobacterium psychrophilum. Flavobacterium psychrophilum is the causative agent of cold water disease in salmon and trout, which is responsible for…

Desulfovibrio…
Dataset

Desulfovibrio vulgaris

Presents the complete genome sequence of the Desulfovibrio vulgaris, a member…

Presents the complete genome sequence of the Desulfovibrio vulgaris, a member of sulfate-reducing bacteria (SRB) commonly found in a variety of soil and aquatic environments. The D. vulgaris…

Salmonella…
Dataset

Salmonella Typhi

Presents the whole sequenced genome of Salmonella enterica serovar Typhi (S.…

Presents the whole sequenced genome of Salmonella enterica serovar Typhi (S. typhi). S. Typhi is the aetiological agent of typhoid fever, a serious invasive bacterial disease of humans with an annual…

IMG
Dataset

IMG Integrated Microbial Genomes

Offers a collection of genomes from all three domains of life, as well as…

Offers a collection of genomes from all three domains of life, as well as viruses, plasmids and genome fragments. IMG contains biosynthetic clusters of genes associated with pathways involved in the…

Xanthomonas…
Dataset

Xanthomonas campestris

Presents the whole sequenced genome of Xanthomonas campestris. X. campestris is…

Presents the whole sequenced genome of Xanthomonas campestris. X. campestris is a major cause of black rot in crucifers, a disease that results in massive tissue degeneration. The type strain was…

Thermotoga…
Dataset

Thermotoga maritima

Presents the whole sequenced genome of Thermotoga maritima. T. maritima is a…

Presents the whole sequenced genome of Thermotoga maritima. T. maritima is a hyperthermophile with an optimum growth temperature of 80°C. The type strain T. maritima MSB8 was isolated from…

Rickettsia…
Dataset

Rickettsia prowazekii

Presents the whole sequenced genome of the obligate intracellular parasite…

Presents the whole sequenced genome of the obligate intracellular parasite Rickettsia prowazekii, the causative agent of epidemic typhus. This genome contains 834 protein-coding genes. The functional…

Mycobacterium…
Dataset

Mycobacterium leprae

Contains the entire genome of Mycobacterium leprae TN. Mycobacterium leprae has…

Contains the entire genome of Mycobacterium leprae TN. Mycobacterium leprae has the longest doubling time of all known bacteria and has thwarted every effort at culture in the laboratory. It is the…

Leptospira…
Dataset

Leptospira interrogans

Reports the complete genomic sequence of a representative virulent serovar type…

Reports the complete genomic sequence of a representative virulent serovar type strain of Leptospira interrogans serogroup Icterohaemorrhagiae consisting of a 4.33-megabase large chromosome and a…

Borreliella…
Dataset

Borreliella burgdorferi

Contains a linear chromosome of 910,725 base pairs and at least 17 linear and…

Contains a linear chromosome of 910,725 base pairs and at least 17 linear and circular plasmids with a combined size of more than 533,000 base pairs. Borrelia burgdorferi is the causative agent of…

Bacillus cereus
Dataset

Bacillus cereus

Reports the sequencing and analysis of the type strain Bacillus cereus ATCC…

Reports the sequencing and analysis of the type strain Bacillus cereus ATCC 14579. Bacillus cereus is an opportunistic pathogen causing food poisoning manifested by diarrheal or emetic syndromes. It…

Aquifex…
Dataset

Aquifex aeolicus

Contains the complete genome sequence of 1,551,335 base pairs of the…

Contains the complete genome sequence of 1,551,335 base pairs of the evolutionarily and physiologically interesting organism. Aquifex aeolicus was one of the earliest diverging, and is one of the…

Yersinia pestis
Dataset

Yersinia pestis

Offers assembly and gene annotation of Yersinia pestis, which is in the…

Offers assembly and gene annotation of Yersinia pestis, which is in the Enterobacteriaceae family. Yersiniae consist of 11 species that have been traditionally distinguished by DNA-DNA hybridisation…

Bacteroides…
Dataset

Bacteroides thetaiotaomicron

Performs whole genome transcriptional profiling of E. rectale and Bacteroides…

Performs whole genome transcriptional profiling of E. rectale and Bacteroides thetaiotaomicron after colonization of gnotobiotic mice with each organism alone, or in combination under 3 dietary…

Agrobacterium…
Dataset

Agrobacterium fabrum

Consists of a circular chromosome, a linear chromosome, and two plasmids.…

Consists of a circular chromosome, a linear chromosome, and two plasmids. Agrobacterium fabrum facilitates investigations into the molecular basis of pathogenesis and the evolutionary divergence of…

Enterococcus…
Dataset

Enterococcus faecalis

Presents the whole sequenced genome of Enterococcus faecalis. E. faecalis is an…

Presents the whole sequenced genome of Enterococcus faecalis. E. faecalis is an important nosocomial pathogen. The type strain E. faecalis V583 is a vancomycin-resistant clinical isolate. The genome…

Legionella…
Dataset

Legionella pneumophila

Presents the genomic sequence of Legionella pneumophila, the bacterial agent of…

Presents the genomic sequence of Legionella pneumophila, the bacterial agent of Legionnaires’ disease, a potentially fatal pneumonia acquired from aerosolized contaminated fresh water. Legionella…

Deinococcus…
Dataset

Deinococcus radiodurans

Presents the complete genome sequence of the radiation resistant bacterium…

Presents the complete genome sequence of the radiation resistant bacterium Deinococcus radiodurans R1. D. radiodurans represents an organism in which all systems for DNA repair, DNA damage export,…

Chlamydia…
Dataset

Chlamydia pneumoniae

Presents the complete sequence of Chlamydia pneumoniae. C. pneumoniae is a…

Presents the complete sequence of Chlamydia pneumoniae. C. pneumoniae is a newly recognized species of Chlamydia that is a natural pathogen of humans, and causes pneumonia and bronchitis. Comparison…

Bordetella…
Dataset

Bordetella pertussis

Includes the genome of Bordetella parapertussis 12822 (4,773,551 bp; 4,404…

Includes the genome of Bordetella parapertussis 12822 (4,773,551 bp; 4,404 genes). Bordetella pertussis is related to Gram-negative β-proteobacteria that colonize the respiratory tracts of mammals.…

TBDB
Dataset

TBDB TuBerculosis DataBase

An online database providing integrated access to genome sequence, expression…

An online database providing integrated access to genome sequence, expression data and literature curation for tuberculosis (TB). TBDB currently houses genome assemblies for numerous strains of…

proGenomes
Dataset

proGenomes

Provides user-friendly access to currently 25 038 high-quality genomes whose…

Provides user-friendly access to currently 25 038 high-quality genomes whose sequences and consistent annotations can be retrieved individually or by taxonomic clade. These genomes are assigned to…

Vibrio…
Dataset

Vibrio parahaemolyticus

Presents the whole sequenced genome of Vibrio parahaemolyticus. V.…

Presents the whole sequenced genome of Vibrio parahaemolyticus. V. parahaemolyticus is a worldwide cause of food-borne gastroenteritis, a pathogenic mechanism distinct from that of V cholerae. The V.…

Shewanella…
Dataset

Shewanella oneidensis

Presents the whole sequenced genome of Shewanella oneidensis. Interest in this…

Presents the whole sequenced genome of Shewanella oneidensis. Interest in this microorganism is due to its respiratory versatility and ability to reduce a number of toxic metals and radionuclides.…

Bacillus…
Dataset

Bacillus anthracis

Contains the whole-genome shotgun (WGS) sequencing of the Bacillus anthracis…

Contains the whole-genome shotgun (WGS) sequencing of the Bacillus anthracis STI isolate. This genome was obtained by the Illumina GAIIx sequencing platform. Bacillus anthracis is a pathogenic…

DarkHorse HGT…
Dataset

DarkHorse HGT Candidate Resource

Gathers information about explore HGT patterns for individual genes, genomes,…

Gathers information about explore HGT patterns for individual genes, genomes, or groups of genomes. DarkHouse includes simple selection tools for individual organisms or groups of organisms, and…

Ensembl Genomes
Dataset

Ensembl Genomes

An integrating resource for genome-scale data from non-vertebrate species.

An integrating resource for genome-scale data from non-vertebrate species.

BacMap
Dataset

BacMap

Provides several information about sequenced bacterial genomes. BacMap is a…

Provides several information about sequenced bacterial genomes. BacMap is a database including a searchable mode and some maps about sequenced bacterial (more than 1500). It treats mostly all…

Chlamydia…
Dataset

Chlamydia trachomatis

Presents the complete sequence of Chlamydia trachomatis, the most common cause…

Presents the complete sequence of Chlamydia trachomatis, the most common cause of sexually transmitted infections. C. trachomatis isolates are classified serologically with 15 serovariants, based on…

MicrobesOnline
Dataset

MicrobesOnline

Includes over 1000 complete genomes of bacteria, archaea and fungi and…

Includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms. To assist in annotating genes and in reconstructing their…

Haemophilus…
Dataset

Haemophilus influenzae

Presents the whole sequenced genome of Haemophilus influenzae. H. influenzae is…

Presents the whole sequenced genome of Haemophilus influenzae. H. influenzae is an opportunistic bacterial pathogen. H. influenzae was mistakenly considered to be the cause of influenza when it was…

IMG/M
Dataset

IMG/M Integrated Microbial Genomes with Microbiome Samples

A database for analysis and annotation of genome and metagenome datasets in a…

A database for analysis and annotation of genome and metagenome datasets in a comprehensive comparative context. IMG/M includes archaea, bacteria, eukarya, plasmids, viruses, genome fragments…

Campylobacter…
Dataset

Campylobacter jejuni

Presents the complete sequence of Campylobacter jejuni, the leading bacterial…

Presents the complete sequence of Campylobacter jejuni, the leading bacterial cause of human gastroenteritis in the developed world. To improve our understanding of this important human pathogen, the…

HGT-DB
Dataset

HGT-DB Horizontal Gene Transfer DataBase

A genomic database that includes statistical parameters such as G+C content,…

A genomic database that includes statistical parameters such as G+C content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complete…

TADB
Dataset

TADB

A web-based resource for Type 2 toxin-antitoxin loci in Bacteria and Archaea.

A web-based resource for Type 2 toxin-antitoxin loci in Bacteria and Archaea.

RhizoBase
Dataset

RhizoBase

A genome database for rhizobia, nitrogen-fixing bacteria associated with…

A genome database for rhizobia, nitrogen-fixing bacteria associated with leguminous plants.

CCDB
Dataset

CCDB CyberCell DataBase

A comprehensive collection of detailed enzymatic, biological, chemical,…

A comprehensive collection of detailed enzymatic, biological, chemical, genetic, and molecular biological data about E. coli (strain K12, MG1655).

MvirDB
Dataset

MvirDB

Integrates DNA and protein sequence information from Tox-Prot, SCORPION, the…

Integrates DNA and protein sequence information from Tox-Prot, SCORPION, the PRINTS virulence factors, VFDB, TVFac, Islander, ARGO and a subset of VIDA.

EcoGene
Dataset

EcoGene

A database and website devoted to continuously improving the structural and…

A database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12.

Geobacter…
Dataset

Geobacter sulfurreducens

Presents the whole sequenced genome of Geobacter sulfurreducens. G.…

Presents the whole sequenced genome of Geobacter sulfurreducens. G. sulfurreducens is one of the predominant metal-reducing bacteria found in subsurface communities. It is capable of oxidizing…

NMPDR
Dataset

NMPDR National Microbial Pathogen Data Resource

Compiles information about NIAID Category B priority pathogens, including the…

Compiles information about NIAID Category B priority pathogens, including the food and water-borne diarrheagenic bacteria. NMPDR collects multiple data about pathogenic microorganisms and includes a…

ICEberg
Dataset

ICEberg

A web-based resource for integrative and conjugative elements found in Bacteria.

A web-based resource for integrative and conjugative elements found in Bacteria.

OriDB
Dataset

OriDB DNA replication Origin DataBase

Provides a catalogue of confirmed and predicted DNA replication origin sites.

Provides a catalogue of confirmed and predicted DNA replication origin sites.

GenProtEC
Dataset

GenProtEC

Dedicated to the functions encoded by the Escherichia coli K-12 (strain MG1655)…

Dedicated to the functions encoded by the Escherichia coli K-12 (strain MG1655) genome.

PortEco
Dataset

PortEco

A next-generation data resource for the bacterial model organism, Escherichia…

A next-generation data resource for the bacterial model organism, Escherichia coli.

MolliGen
Dataset

MolliGen

A database dedicated to the comparative genomics of bacteria belonging to the…

A database dedicated to the comparative genomics of bacteria belonging to the class Mollicutes.

HGTree
Dataset

HGTree

Provides pre-calculated horizontal gene transfer (HGT) events in prokaryotic…

Provides pre-calculated horizontal gene transfer (HGT) events in prokaryotic genomes (Archaea and Bacteria). HGTree defines lateral gene transfer by comparing the gene tree for each orthologous gene…

Genolist
Dataset

Genolist An Integrated Environment for the Analysis of Microbial Genomes

Gathers multitude of published bacterial genomes. Genolist aims to perform data…

Gathers multitude of published bacterial genomes. Genolist aims to perform data analysis in a comparative genomics context. The database allows users to access to supplement public genome data with…

UCSC Archaeal…
Dataset

UCSC Archaeal Genome Browser

Offers a graphical web-based resource for exploration and discovery within…

Offers a graphical web-based resource for exploration and discovery within archaeal and other selected microbial genomes.

ATGC
Dataset

ATGC Alignable Tight Genomic Clusters

A database of closely related microbial genomes optimized for microevolutionary…

A database of closely related microbial genomes optimized for microevolutionary research.

ASAP
Dataset

ASAP A Systematic Annotation Package

A comprehensive web-based system for community genome annotation and analysis.

A comprehensive web-based system for community genome annotation and analysis.

HEG-DB
Dataset

HEG-DB Highly Expressed Genes DataBase

A genomic database that includes the prediction of which genes are highly…

A genomic database that includes the prediction of which genes are highly expressed in prokaryotic complete genomes under strong translational selection.

AgBase
Dataset

AgBase

Provides resources to facilitate modeling of functional genomics data and…

Provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes.

Clostridioides…
Dataset

Clostridioides difficile

Presents the complete genome sequence of Clostridium difficile strain 630, a…

Presents the complete genome sequence of Clostridium difficile strain 630, a virulent and multidrug-resistant strain. A large proportion (11%) of the genome consists of mobile genetic elements,…

PEDANT
Dataset

PEDANT

Provides exhaustive automatic analysis of genomic sequences by a large variety…

Provides exhaustive automatic analysis of genomic sequences by a large variety of bioinformatics tools. PEDANT is a database that includes (i) integration with the BioRSTM data retrieval system which…

ProPortal
Dataset

ProPortal

A database containing genomic, metagenomic, transcriptomic and field data for…

A database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus.

ICDS database
Dataset

ICDS database Interrupted CoDing Sequence database

Contains interrupted coding sequence detected by a similarity-based approach in…

Contains interrupted coding sequence detected by a similarity-based approach in 80 complete prokaryotic genomes.

ShiBASE
Dataset

ShiBASE

It focuses on the comparative genomics of Shigella and provides a way to…

It focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format.

EcoliWiki
Dataset

EcoliWiki

Generates community-based pages about everything related to non-pathogenic E.…

Generates community-based pages about everything related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.

CauloBrowser
Dataset

CauloBrowser

An online resource for Caulobacter studies. CauloBrowser provides a…

An online resource for Caulobacter studies. CauloBrowser provides a user-friendly interface for quickly searching genes of interest and downloading genome-wide results. Search results about…

MBGD
Dataset

MBGD Microbial genome database for comparative analysis

A comprehensive ortholog database for flexible comparative analysis of…

A comprehensive ortholog database for flexible comparative analysis of microbial genomes, where the users are allowed to create an ortholog table among any specified set of organisms. The MyMBGD…

DBETH
Dataset

DBETH Database for Bacterial ExoToxins

The main objective of this database is to provide a comprehensive knowledgebase…

The main objective of this database is to provide a comprehensive knowledgebase for human pathogenic bacterial toxins where various important sequence, structure and physico-chemical property based…

LEGER
Dataset

LEGER

Supports functional Listeria genome analyses by combining information obtained…

Supports functional Listeria genome analyses by combining information obtained by applying bioinformatics methods and from public databases to improve the original annotations. LEGER offers three…

BrucellaBase
Dataset

BrucellaBase

A web-based platform that provides features of a genome database together with…

A web-based platform that provides features of a genome database together with unique analysis tools. We have developed a web version of the multilocus sequence typing (MLST) and phylogenetic…

AlterORF
Dataset

AlterORF

Provides a platform for improving genome annotation and to serve as an aid for…

Provides a platform for improving genome annotation and to serve as an aid for the identification of prokaryotic genes that potentially encode proteins in more than one reading frame.

SalFoS
Dataset

SalFoS Salmonella Foodborne Syst-OMICS database

Provides metadata, including phenotypic as well as genomic data, for isolates…

Provides metadata, including phenotypic as well as genomic data, for isolates of the collection. SalFoS is a database where goals are to understand how Salmonella evolves over time, improve the…

MetaMicrobesOnl…
Dataset

MetaMicrobesOnline

Offers phylogenetic analysis of genes from microbial genomes and metagenomes.

Offers phylogenetic analysis of genes from microbial genomes and metagenomes.

CyanoLyase
Dataset

CyanoLyase

A manually curated sequence and amino acid motif database gathering all the…

A manually curated sequence and amino acid motif database gathering all the different phycobilin lyases and related protein sequences available in public databases. CyanoLyase provides an extensive…

MyMpn
Dataset

MyMpn

An online resource devoted to studying the human pathogen Mycoplasma…

An online resource devoted to studying the human pathogen Mycoplasma pneumoniae, a minimal bacterium causing lower respiratory tract infections. MyMpn hosts a wealth of omics-scale datasets generated…

BuchneraBASE
Dataset

BuchneraBASE

A database designed to encapsulate and reference information obtained from the…

A database designed to encapsulate and reference information obtained from the complete genome sequence of the gamma-proteobacterium Buchnera aphidicola APS.

Amycolatopsis…
Dataset

Amycolatopsis mediterranei

Is used for industry-scale production of rifamycin, which plays a vital role in…

Is used for industry-scale production of rifamycin, which plays a vital role in antimycobacterial therapy. Amycolatopsis mediterranei comprises 10 236 715 base pairs and is one of the largest…

Strepto-DB
Dataset

Strepto-DB

A database for comparative genomics of group A and group B streptococci.

A database for comparative genomics of group A and group B streptococci.

BµG@Sbase
Dataset

BµG@Sbase

Contains microbial gene expression and comparative genomic hybridization…

Contains microbial gene expression and comparative genomic hybridization experimental data. BµG@Sbase is a web-browsable Minimum Information about a Microarray Experiment (MIAME)-compliant database…

Citrus…
Dataset

Citrus Greening Solutions

Provides gene set of the D. citri which includes 530 manually curated genes and…

Provides gene set of the D. citri which includes 530 manually curated genes and about 20,000 genes. Citrus Greening Solutions offers solution that uses a therapeutic delivery strategy and citrus…

KEGG GENES
Dataset

KEGG GENES

Provides a collection of completely sequenced genomes. KEGG GENES contains gene…

Provides a collection of completely sequenced genomes. KEGG GENES contains gene catalogs mainly generated from NCBI RefSeq and GenBank. The database is enriched with a set of metagenome data and…

Listeriomics
Dataset

Listeriomics

Integrates different tools for omics data analyses. Listeriomics integrates all…

Integrates different tools for omics data analyses. Listeriomics integrates all the complete Listeria species genomes, transcriptomes, and proteomes published to date. It allows navigation among all…

SilkPathDB
Dataset

SilkPathDB

Proposes a comprehensive resource for studying on pathogens of silkworm,…

Proposes a comprehensive resource for studying on pathogens of silkworm, including microsporidia, fungi, bacteria and virus. SilkPathDB provides access to not only genomic data including functional…

BioCyc
Dataset

BioCyc

Allows users to search information about pathway/genomes. BioCyc is a database…

Allows users to search information about pathway/genomes. BioCyc is a database that mixes thousands of genomes with additional information curated from the biomedical literature by biologist…

BorreliaBase
Dataset

BorreliaBase

An online database for comparative browsing of borrelia genomes. BorreliaBase…

An online database for comparative browsing of borrelia genomes. BorreliaBase is currently populated with sequences from 35 genomes of eight lyme-borreliosis group borrelia species and 7…

Mycoplasma…
Dataset

Mycoplasma mycoides

Contains 985 putative genes of Mycoplasma mycoides, of which 72 are part of…

Contains 985 putative genes of Mycoplasma mycoides, of which 72 are part of insertion sequences and encode transposases. Mycoplasma mycoides is the causative agent of contagious bovine…

Lactococcus…
Dataset

Lactococcus lactis

Contains 2,365,589 base pairs and encodes 2310 proteins, including 293…

Contains 2,365,589 base pairs and encodes 2310 proteins, including 293 protein-coding genes belonging to six prophages and 43 insertion sequence (IS) elements of Lactococcus lactis. Lactococcus…

Clostridium…
Dataset

Clostridium botulinum

Presents the complete genome sequence of Clostridium botulinum and related…

Presents the complete genome sequence of Clostridium botulinum and related clostridial species express extremely potent neurotoxins known as botulinum neurotoxins. C. botulinum causes long-lasting,…

Caulobacter…
Dataset

Caulobacter crescentus

Presents the complete sequence of Caulobacter crescentus which grows in a…

Presents the complete sequence of Caulobacter crescentus which grows in a dilute aquatic environment and coordinates the cell division cycle and multiple cell differentiation events. Caulobacter…

Natto Genome
Dataset

Natto Genome

Provides the whole genome sequence of Bacillus subtilis natto with detailed…

Provides the whole genome sequence of Bacillus subtilis natto with detailed analyses of a set of genes related to natto production and demonstrating the number and locations of insertion sequences. A…

CKB
Dataset

CKB Cyanobacterial KnowledgeBase

A free access database that contains the genomic and proteomic information of…

A free access database that contains the genomic and proteomic information of 74 fully sequenced cyanobacterial genomes belonging to seven orders. CKB also contains tools for sequence analysis. The…

Cryptosporidium…
Dataset

Cryptosporidium hominis Gene Catalog

Gathers information about C. hominis TU502 predicted genes. Cryptosporidium…

Gathers information about C. hominis TU502 predicted genes. Cryptosporidium hominis genes furnishes a set composed of 3745 protein-coding genes which allows new in silico analyses to identify…

MegaBac
Dataset

MegaBac

Integrates obtained theoretical and experimental data. MegaBac is a…

Integrates obtained theoretical and experimental data. MegaBac is a bioinformatical platform to facilitate comparative genome analysis of B. megaterium. This database has been set up using genomic…

Gloeobacter…
Dataset

Gloeobacter violaceus

Presents the whole sequenced genome of Gloeobacter violaceus. G. violaceus is…

Presents the whole sequenced genome of Gloeobacter violaceus. G. violaceus is an obligate photoautotroph that lacks thylakoid membranes. It has been predicted that G. violaceus diverged in the…

Bradyrhizobium…
Dataset

Bradyrhizobium diazoefficiens

Presents the complete nucleotide sequence of the genome of a symbiotic…

Presents the complete nucleotide sequence of the genome of a symbiotic bacterium Bradyrhizobium diazoefficiens USDA110. Bradyrhizobium diazoefficiens is a symbiotic bacterium that plays an important…

SKB
Dataset

SKB Shewanella knowledgebase

Facilitates manual curation of all sequenced Shewanella genomes. SKB is a…

Facilitates manual curation of all sequenced Shewanella genomes. SKB is a multi-genome annotation environment consisting of ortholog and genome editors. It combines many independent data sources for…

DIGAP
Dataset

DIGAP Database of Improved Gene Annotation for Phytopathogens

Provides annotations for the sequenced bacterial phytopathogen genomes. DIGAP…

Provides annotations for the sequenced bacterial phytopathogen genomes. DIGAP is supported with a user-friendly designed web interface allowing users to search by gene name, DIGAP_ID, PID and gene…

Vibrio fischeri
Dataset

Vibrio fischeri

Presents the whole sequenced genome of Vibrio fischeri. V. fischeri is a…

Presents the whole sequenced genome of Vibrio fischeri. V. fischeri is a non-pathogenic bacterium primarily found in marine environments. V. fischeri is closely related to the pathogenic Vibrio…

Rhodopirellula…
Dataset

Rhodopirellula baltica

Presents the whole sequenced genome of a member of Pirellula sp. strain 1 also…

Presents the whole sequenced genome of a member of Pirellula sp. strain 1 also known as Rhodopirellula baltica. R baltica is a marine representative of the globally distributed and environmentally…

Coxiella…
Dataset

Coxiella burnetii

Presents the complete genome sequence of the 1,995,275-bp genome of Coxiella…

Presents the complete genome sequence of the 1,995,275-bp genome of Coxiella burnetii, a highly virulent zoonotic pathogen and category B bioterrorism agent. The genome of C. burnetii Nine Mile phase…

Neocaridina…
Dataset

Neocaridina denticulata

Offers gene annotation of Neocaridina denticulata also known as Red Cherry…

Offers gene annotation of Neocaridina denticulata also known as Red Cherry shrimp. A library of 170-bp nominal fragment size was constructed from DNA and sequenced using the Illumina HiSeq2000…

Lactobacillus…
Dataset

Lactobacillus plantarum

Identifies the entire genome of Lactobacillus plantarum WCFS1. In Lactobacillus…

Identifies the entire genome of Lactobacillus plantarum WCFS1. In Lactobacillus plantarum database, 116 nucleotide corrections and improved function prediction for nearly 1,200 proteins was…

Esox Lucius
Dataset

Esox Lucius

Offers gene annotation of Esox Lucius also known as northern pike. The northern…

Offers gene annotation of Esox Lucius also known as northern pike. The northern pike genome sequence is composed of 94,267 contigs (N50 = 16,909 bp) contained in 5,688 scaffolds (N50 = 700,535 bp);…

UCSC microbial…
Web

UCSC microbial genome browser

Provides access to more than 400 microbial species from Archaea and Bacteria.…

Provides access to more than 400 microbial species from Archaea and Bacteria. UCSC Genome Browser provides a rapid and reliable display of any requested portion of genomes at any scale, together with…

Mycobacterium…
Dataset

Mycobacterium smegmatis

Reports the whole genome sequences of a Mycobacterium smegmatis laboratory…

Reports the whole genome sequences of a Mycobacterium smegmatis laboratory wild-type strain (MC2 155) and mutants (4XR1, 4XR2) resistant to isoniazid. Mycobacterium smegmatis is a soil dwelling…

CyanoClust
Dataset

CyanoClust

A database of homolog groups in cyanobacteria and plastids that are produced by…

A database of homolog groups in cyanobacteria and plastids that are produced by the program Gclust. CyanoClust contains protein homology information for 38 cyanobacteria, 59 plastids and 1 Paulinella…

SymbioGenomesDB
Dataset

SymbioGenomesDB

Consists of a community database resource for laboratories which aim to…

Consists of a community database resource for laboratories which aim to research and gather information of the genetics and the genomic systems involved in symbiosis, regardless of its biotic…

mycoCLAP
Dataset

mycoCLAP

A searchable database of fungal and bacterial genes encoding…

A searchable database of fungal and bacterial genes encoding lignocellulose-active proteins that have been biochemically characterized. All the biochemical properties and functional annotations…

CyanOmics
Dataset

CyanOmics

A database based on the results of Synechococcus sp. PCC 7002 omics studies.…

A database based on the results of Synechococcus sp. PCC 7002 omics studies. CyanOmics comprises one genomic dataset, 29 transcriptomic datasets and one proteomic dataset and should prove useful for…

Pseudomonas…
Dataset

Pseudomonas putida

Presents the whole sequenced genome of Pseudomonas putida, a metabolically…

Presents the whole sequenced genome of Pseudomonas putida, a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. Sequence…

Moorella…
Dataset

Moorella thermoacetica

Describes the genome sequence of Moorella thermoacetica (f. Clostridium…

Describes the genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum), which is the model acetogenic bacterium that has been widely used for elucidating the WoodLjungdahl pathway of…

PolyTB
Dataset

PolyTB

A web-based resource designed to explore Mycobacterium tuberculosis complex…

A web-based resource designed to explore Mycobacterium tuberculosis complex (MTBC) genomic variation at a global scale.

AceDB
Dataset

AceDB A C. elegans DataBase

Provides a custom database kernel, with a non-standard data model designed…

Provides a custom database kernel, with a non-standard data model designed specifically for handling scientific data flexibly, and a graphical user interface with many specific displays and tools for…

SPGDB
Dataset

SPGDB Streptococcus pneumoniae Genome Database

Integrates and analyzes the completely sequenced and available S. pneumoniae…

Integrates and analyzes the completely sequenced and available S. pneumoniae genome sequences. Further, links to several tools are provided to compare the pool of gene and protein sequences, and…

Thermosynechoco…
Dataset

Thermosynechococcus elongatus

Presents the whole sequenced genome of Thermosynechococcus elongatus. T.…

Presents the whole sequenced genome of Thermosynechococcus elongatus. T. elongatus is a thermophilic cyanobacterium. This organism is readily transformable making it useful for molecular analyses. T.…

Mesorhizobium…
Dataset

Mesorhizobium ciceri

Describes the genome of Mesorhizobium ciceri bv. biserrulae strain WSM1271T…

Describes the genome of Mesorhizobium ciceri bv. biserrulae strain WSM1271T consisting of a 6,264,489 bp chromosome and a 425,539 bp plasmid that together encode 6,470 protein-coding genes and 61 RNA…

GORBI
Dataset

GORBI

Presents the results of a novel model for computational assignment of gene…

Presents the results of a novel model for computational assignment of gene function using phylogenetic profiling. The predictions for 998 prokaryotic genomes include ~400000 high-confidence…

Chloroflexus…
Dataset

Chloroflexus aurantiacus

Presents the complete sequence of Chloroflexus aurantiacus, a thermophilic…

Presents the complete sequence of Chloroflexus aurantiacus, a thermophilic filamentous anoxygenic phototrophic (FAP) bacterium. Cfl. aurantiacus can grow phototrophically under anaerobic conditions…

Bordetella…
Dataset

Bordetella parapertussis

Includes the whole genome of Bordetella parapertussis Bpp5. The bacteria can…

Includes the whole genome of Bordetella parapertussis Bpp5. The bacteria can cause bronchitis and others respiratory diseases. The classical Bordetella subspecies are phylogenetically closely…

Bordetella…
Dataset

Bordetella bronchiseptica

Contains the whole genome of Bordetella bronchiseptica 253. Bordetella…

Contains the whole genome of Bordetella bronchiseptica 253. Bordetella bronchiseptica causes bronchitis and other respiratory diseases. The classical Bordetella subspecies are phylogenetically…

Staphylococcus…
Dataset

Staphylococcus epidermidis

Presents the whole sequenced genome of Staphylococcus epidermidis. S.…

Presents the whole sequenced genome of Staphylococcus epidermidis. S. epidermidis strains are diverse in their pathogenicity. Some are invasive and cause serious nosocomial infections, whereas others…

Neisseria…
Dataset

Neisseria gonorrhoeae

Reports the whole genome of Neisseria gonorrhoeae FA 1090. A potential…

Reports the whole genome of Neisseria gonorrhoeae FA 1090. A potential multilocus sequence typing for N. gonorrhoeae, based on 500- to 600-bp gene fragments of seven housekeeping gene loci, would…

Streptococcus…
Dataset

Streptococcus sanguinis

Presents the whole sequenced genome of Streptococcus sanguinis. S. sanguinis is…

Presents the whole sequenced genome of Streptococcus sanguinis. S. sanguinis is an indigenous gram-positive bacterium that has been recognized for a long time as a key player in colonization of the…

Klebsiella…
Dataset

Klebsiella pneumoniae

Presents the whole sequenced genome of Klebsiella pneumoniae. K. pneumoniae is…

Presents the whole sequenced genome of Klebsiella pneumoniae. K. pneumoniae is the most medically important organism within the genus Klebsiella. It usually causes pneumonia in immunocompromised…

Ketogulonicigen…
Dataset

Ketogulonicigenium vulgare

Presents the whole sequenced genome of Ketogulonigenium vulgarum. K. vulgarum…

Presents the whole sequenced genome of Ketogulonigenium vulgarum. K. vulgarum WSH-001 is an industrial organism commonly used in the production of vitamin C. K. vulgarum converts the substrate…

Fusobacterium…
Dataset

Fusobacterium nucleatum

Presents the whole sequenced genome of Fusobacterium nucleatum. Fusobacterium…

Presents the whole sequenced genome of Fusobacterium nucleatum. Fusobacterium nucleatum is the dominant bacterial species in oral cavity. F. nucleatum subsp. nucleatum ATCC 25586 is the type strain…

Enterobacter…
Dataset

Enterobacter cloacae

Presents the whole sequenced genome of Enterobacter cloacae. E. cloacae is an…

Presents the whole sequenced genome of Enterobacter cloacae. E. cloacae is an important nosocomial pathogen. The type strain E. cloacae subsp. cloacae ATCC 13047 was isolated from human cerebrospinal…

Enterobacter…
Dataset

Enterobacter aerogenes

Presents the whole sequenced genome of Enterobacter aerogenes. E. aerogenes is…

Presents the whole sequenced genome of Enterobacter aerogenes. E. aerogenes is an opportunistic human pathogen. This is the first complete genome sequence of the Enterobacter aerogenes species. The…

Clostridium…
Dataset

Clostridium acetobutylicum

Presents the complete genome sequence of Clostridium acetobutylicum. The genome…

Presents the complete genome sequence of Clostridium acetobutylicum. The genome consists of a 3.94-Mb chromosome and a 192-kb megaplasmid that contains the majority of genes responsible for solvent…

Bacillus…
Dataset

Bacillus thuringiensis

Reports the sequencing and comparative analysis of the genomes of two members…

Reports the sequencing and comparative analysis of the genomes of two members of the Bacillus cereus group, Bacillus thuringiensis 97-27 subsp. konkukian serotype H34, isolated from a necrotic human…