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Taxonomy browser (Bacteria)

Bacteria

Taxonomy ID: 2 (for references in articles please use NCBI:txid2)
Scientific name: Bacteria
Genbank common name: eubacteria
Rank: superkingdom
Genetic code: Translation table 11 (Bacterial, Archaeal and Plant Plastid)
Other names:
in-part: Monera
in-part: Procaryotae
in-part: Prokaryota
in-part: Prokaryotae
in-part: prokaryote
in-part: prokaryotes
blast name: bacteria
Lineage( full )
cellular organisms
   Entrez records   
Database name Subtree links Direct links
Nucleotide 53,457,870 24
Protein 596,202,011 23,084
Structure 52,748 -
Genome 24,354 -
Popset 61,858 12,117
Conserved Domains 19,420 8,683
GEO Datasets 84,897 1,934
PubMed Central 719,464 -
Gene 12,447,536 -
SRA Experiments 939,366 1,567
GEO Profiles 904,754 -
Protein Clusters 942,125 11,385
Identical Protein Groups 163,028,547 23,084
Bio Project 88,740 250
Bio Sample 1,104,990 1,452
Bio Systems 784,143 -
Assembly 224,726 -
Probe 38,178 54
PubChem BioAssay 103,776 93
Taxonomy 491,139 1

Comments and References:

Bacteria
When Carl Woese first set forth the three-domain classification of life, he proposed the names "Archaebacteria" and "Eubacteria" for the two prokaryotic domains. These were replaced with the names "Archaea" and "Bacteria" in Woese et al. (1990). The taxonomic name "Bacteria" refers only to the eubacteria. The informal name "bacteria" is occasionally used loosely in the literature to refer to all of the prokayrotes, and care should be taken to interpret it's meaning in any particular context.

Reference to PubMed documentAchenbach-Richter L et al. (1987)
Achenbach-Richter, L., Gupta, R., Stetter, K.O., and Woese, C.R. "Were the original eubacteria thermophiles?" Syst. Appl. Microbiol. (1987) 9:34-39.

Reference to PubMed documentChristensen H et al. (2000)
Christensen, H., Angen, O., Mutters, R., Olsen, J.E., and Bisgaard, M. "DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA." Int. J. Syst. Evol. Microbiol. (2000) 50:1095-1102.

Reference to PubMed documentChristensen H et al. (2001)
Christensen, H., Bisgaard, M., Frederiksen, W., Mutters, R., Kuhnert, P., and Olsen, J.E. "Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify recommendation 30b of the Bacteriological Code (1990 Revision)." Int. J. Syst. Evol. Microbiol. (2001) 51:2221-2225.

Reference to PubMed documentClayton RA et al. (1995)
Clayton, R.A., Sutton, G., Hinkle, P.S. Jr, Bult, C., and Fields, C. "Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa." Int. J. Syst. Bacteriol. (1995) 45:595-599.

Reference to PubMed documentDalevi D et al. (2001)
Dalevi, D., Hugenholtz, P., and Blackall, L.L. "A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data." Int. J. Syst. Evol. Microbiol. (2001) 51:385-391.

Reference to PubMed documentEuzeby JP (1997b)
Euzeby, J.P. "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet." Int. J. Syst. Bacteriol. (1997) 47:590-592.

Reference to PubMed documentGurtler V & Mayall BC (2001)
Gurtler, V., and Mayall, B.C. "Genomic approaches to typing, taxonomy and evolution of bacterial isolates." Int. J. Syst. Evol. Microbiol. (2001) 51:3-16

Haeckel EH (1894)
Haeckel, E.H.: Systematische Phylogenie der Protisten und Planzen. (1894) I.G. Reimer, Berlin. p. 40.

Reference to PubMed documentHansmann S & Martin W (2000)
Hansmann, S., and Martin, W. "Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis." Int. J. Syst. Evol. Microbiol. (2000) 50:1655-1663.

Reference to PubMed documentKeswani J & Whitman WB (2001)
Keswani, J., and Whitman, W.B. "Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes." Int. J. Syst. Evol. Microbiol. (2001) 51:667-678.

Reference to PubMed documentMoore LV et al. (1994b)
Moore, L.V., Bourne, D.M., and Moore, W.E. "Comparative distribution and taxonomic value of cellular fatty acids in thirty-three genera of anaerobic gram-negative bacilli." Int. J. Syst. Bacteriol. (1994) 44:338-347.

Reference to PubMed documentMurray RG & Schleifer KH (1994)
Murray, R.G., and Schleifer, K.H. "Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes." Int. J. Syst. Bacteriol. (1994) 44:174-176.

Reference to PubMed documentPalys T et al. (1997)
Palys, T., Nakamura, L.K., and Cohan, F.M. "Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data." Int. J. Syst. Bacteriol. (1997) 47:1145-1156.

Reference to PubMed documentStackebrandt E et al. (2002)
Stackebrandt, E., Frederiksen, W., Garrity, G.M., Grimont, P.A., Kampfer, P., Maiden, M.C., Nesme, X., Rossello-Mora, R., Swings, J., Truper, H.G., Vauterin, L., Ward, A.C., and Whitman, W.B. "Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology." Int. J. Syst. Evol. Microbiol. (2002) 52:1043-1047.

Reference to PubMed documentTindall BJ (1999b)
Tindall, B.J. "Proposals to update and make changes to the Bacteriological Code." Int. J. Syst. Bacteriol. (1999) 49:1309-1312. [No abstract available.]

Reference to PubMed documentTindall BJ (1999c)
Tindall, B.J. "Misunderstanding the Bacteriological Code." Int. J. Syst. Bacteriol. (1999) 49:1313-1316.

Reference to PubMed documentTindall BJ (1999d)
Tindall, B.J. "Proposal to change Rule 18a, Rule 18f and Rule 30 to limit the retroactive consequences of changes accepted by the ICSB." Int. J. Syst. Bacteriol. (1999) 49:1321-1322. [No abstract available.]

Reference to PubMed documentTindall BJ (1999e)
Tindall, B.J. "Proposal to change the Rule governing the designation of type strains deposited under culture collection numbers allocated for patent purposes." Int. J. Syst. Bacteriol. (1999) 49:1317-1319. [No abstract available.]

Nota BeneTruper HG (1994)
Truper, H.G., "Taxonomic notes: Names for higher taxa and their impact on the Code of Nomenclature of Bacteria." Int. J. Syst. Bacteriol. (1994) 368-369. [No PubMed record available.]

Reference to PubMed documentViale AM et al. (1994)
Viale, A.M., Arakaki, A.K., Soncini, F.C., and Ferreyra, R.G. "Evolutionary relationships among eubacterial groups as inferred from GroEL (chaperonin) sequence comparisons." Int. J. Syst. Bacteriol. (1994) 44:527-533.

Reference to PubMed documentWinker S & Woese CR (1991)
Winker, S., and Woese, C.R. "A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics." Syst. Appl. Microbiol. (1991) 14:305-310.

Reference to PubMed documentWoese CR & Fox GE (1977)
Woese, C.R., and Fox, G.E. "Phylogenetic structure of the prokaryotic domain: the primary kingdoms." Proc. Natl. Acad. Sci. U S A (1977) 74:5088-5090.

Reference to PubMed documentWoese CR et al. (1985)
Woese, C.R., Stackebrandt, E., Macke, T.J., and Fox, G.E. "A phylogenetic definition of the major eubacterial taxa." Syst. Appl. Microbiol. (1985) 6:143-151.

Reference to PubMed documentWoese CR et al. (1990)
Woese, C.R., Kandler, O., and Wheelis, M.L. "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya." Proc. Natl. Acad. Sci. USA (1990) 87:4576-4579.

Reference to PubMed documentXu HX et al. (2000)
Xu, H.X., Kawamura, Y., Li, N., Zhao, L., Li, T.M., Li, Z.Y., Shu, S., and Ezaki, T. "A rapid method for determining the G+C content of bacterial chromosomes by monitoring fluorescence intensity during DNA denaturation in a capillary tube." Int. J. Syst.Evol. Microbiol. (2000) 50:1463-1469.

Reference to PubMed documentYoung JM (2000)
Young, J.M. "Suggestions for avoiding on-going confusion from the Bacteriological Code." Int. J. Syst. Evol. Microbiol. (2000) 50:1687-1689. [No abstract available.]


Genome Information

   Trace records (raw single-pass reads of DNA sequence)   
Sequencing Center Name
Record counts per type
WGS ALL
JGI - Joint Genome Institute, U.S. Department of Energy
71,373 71,373
Totals per type
71,373 71,373

External Information Resources (NCBI LinkOut)

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Bacteria taxonomy taxonomy/phylogenetic Arctos Specimen Database
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10 records from this provider taxonomy/phylogenetic NCBI taxonomy bookmarks
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UCMP taxonomy/phylogenetic UCMP phylogeny exhibit
Bacteria taxonomy/phylogenetic World Register of Marine Species
Wikipedia taxonomy/phylogenetic iPhylo
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