Table 3

Bacterial genomes used in this paper. All phyla in GenBank as of December 2004 are represented. Bold letters give abbreviations used in Table 1.

Specific Genome

Taxonomy (Phylum; Class)


Corynebacterium glutamicum

Actinobacteria;Actinobacteria

Mycobacterium tuberculosis H37Rv

Actinobacteria;Actinobacteria

Bifidobacterium longum

Actinobacteria;Actinobacteria

Streptomyces avermitilis

Actinobacteria;Actinobacteria

Aquifex aeolicus

Aquificae;Aquificae

Bacteroides thetaiotaomicron VPI-5482

Bacteroidetes/Chlorobi;Bacteroidetes

Chlorobium tepidum TLS

Bacteroidetes/Chlorobi;Chlorobi

Porphyromonas gingivalis W83

Bacteroidetes/Chlorobi;Chlorobi

Chlamydia trachomatis

Chlamydiae/Verrucomicrobia;Chlamydiae

Chlamydophila pneumoniae AR39

Chlamydiae/Verrucomicrobia;Chlamydiae

Chloroflexus aurantiacus

Chloroflexi;Chloroflexi

Gloeobacter violaceus

Cyanobacteria;Chroococcales

Synechococcus sp WH8102

Cyanobacteria;Chroococcales

Synechocystis PCC6803

Cyanobacteria;Chroococcales

Nostoc sp

Cyanobacteria;Nostocales

Prochlorococcus marinus MIT9313

Cyanobacteria;Prochlorophytes

Deinococcus radiodurans

Deinococcus-Thermus;Deinococci

Bacillus subtilis

Firmicutes;Bacilli

Oceanobacillus iheyensis

Firmicutes;Bacilli

Listeria monocytogenes

Firmicutes;Bacilli

Staphylococcus aureus subsp. aureus N315

Firmicutes;Bacilli

Lactococcus lactis

Firmicutes;Bacilli

Streptococcus pneumoniae R6

Firmicutes;Bacilli

Clostridium tetani E88

Firmicutes;Clostridia

Thermoanaerobacter tengcongensis

Firmicutes;Clostridia

Mycoplasma

Firmicutes;Mollicutes

Ureaplasma

Firmicutes;Mollicutes

Fusobacterium nucleatum

Fusobacteria;Fusobacteria

Pirellula sp

Planctomycetes;Planctomycetacia

Caulobacter crescentus

Proteobacteria;Alphaproteobacteria

Rhodopseudomonas palustris

Proteobacteria;Alphaproteobacteria

Brucella melitensis

Proteobacteria;Alphaproteobacteria

Bradyrhizobium japonicum

Proteobacteria;Alphaproteobacteria

Mesorhizobium loti

Proteobacteria;Alphaproteobacteria

Rickettsia conorii

Proteobacteria;Alphaproteobacteria

Ralstonia solanacearum

Proteobacteria;Betaproteobacteria

Neisseria meningitidis Z2491

Proteobacteria;Betaproteobacteria

Chromobacterium violaceum

Proteobacteria;Betaproteobacteria

Bordetella pertussis

Proteobacteria;Betaproteobacteria

Nitrosomonas europaea

Proteobacteria;Betaproteobacteria

Coxiella burnetii

Proteobacteria;Gammaproteobacteria

Escherichia coli K12

Proteobacteria;Gammaproteobacteria

Haemophilus influenzae

Proteobacteria;Gammaproteobacteria

Pseudomonas aeruginosa

Proteobacteria;Gammaproteobacteria

Shigella flexneri 2a

Proteobacteria;Gammaproteobacteria

Shewanella oneidensis

Proteobacteria;Gammaproteobacteria

Vibrio cholerae

Proteobacteria;Gammaproteobacteria

Xanthomonas campestris

Proteobacteria;Gammaproteobacteria

Xylella fastidiosa

Proteobacteria;Gammaproteobacteria

Desulfovibrio desulfuricans

Proteobacteria;delta/epsilon subdivisions

Geobacter sulfurreducens

Proteobacteria;delta/epsilon subdivisions

Campylobacter jejuni

Proteobacteria;delta/epsilon subdivisions

Helicobacter pylori J99

Proteobacteria;delta/epsilon subdivisions

Wolinella succinogenes

Proteobacteria;delta/epsilon subdivisions

Borrelia burgdorferi

Spirochaetes;Spirochaetes

Leptospira interrogans

Spirochaetes;Spirochaetes

Treponema pallidum

Spirochaetes;Spirochaetes

Thermotoga maritima

Thermotogae;Thermotogae


Bern and Goldberg BMC Evolutionary Biology 2005 5:34   doi:10.1186/1471-2148-5-34

Open Data