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Taxonomy browser (Archaea)

Archaea

Taxonomy ID: 2157 (for references in articles please use NCBI:txid2157)
Scientific name: "Archaea" Woese et al. 1990, effective name 1)
Rank: superkingdom
Genetic code: Translation table 11 (Bacterial, Archaeal and Plant Plastid)
Other names:
synonym: Mendosicutes
synonym: Metabacteria
synonym: "Archaebacteria" (sic) Woese and Fox 1977, effective name 1)
in-part: Monera
in-part: Procaryotae
in-part: Prokaryota
in-part: Prokaryotae
in-part: prokaryote
in-part: prokaryotes
blast name: archaea
Lineage( full )
cellular organisms
   Entrez records   
Database name Subtree links Direct links
Nucleotide 755,468 5
Nucleotide EST 578 -
Nucleotide GSS 4,668 -
Protein 4,970,585 79
Structure 4,744 2
Genome 1,601 -
Popset 4,077 1,205
Conserved Domains 1,644 643
GEO Datasets 4,397 182
PubMed Central 31,675 12,734
Gene 806,210 -
SRA Experiments 4,083 53
GEO Profiles 9,216 -
Protein Clusters 48,665 -
Identical Protein Groups 3,128,535 2
Bio Project 1,735 9
Bio Sample 6,958 78
Bio Systems 32,115 -
Assembly 3,219 -
Probe 190 5
PubChem BioAssay 84 -
Taxonomy 13,021 1

Notes:

Comments and References:

Reference to PubMed documentAchenbach-Richter L & Woese CR (1988)
Achenbach-Richter, L., and Woese, C.R. "The ribosomal gene spacer region in archaebacteria." Syst. Appl. Microbiol. (1988) 10:211-214.

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

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 documentMcGill TJ et al. (1986)
McGill, T.J., Jurka, J., Sobieski, J.M., Pickett, M.H., Woese, C.R., and Fox, G.E. "Characteristic archaebacterial 16S rRNA oligonucleotides." Syst. Appl. Microbiol. (1986) 7:194-197.

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 documentPetitjean C et al. (2015)
Petitjean, C., Deschamps, P., Lopez-GarcIa, P., and Moreira, D. "Rooting the domain Archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota." Genome Biol. Evol. (2015) 7:191-204.

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 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 & Olsen GJ (1984)
Woese, C.R., and Olsen, G.J. "The phylogenetic relationships of three sulfur dependent archaebacteria." Syst. Appl. Microbiol. (1984) 5:97-105.

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.]

Reference to PubMed documentYoung JM (2001)
Young, J.M. "Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy." Int. J. Syst. Evol. Microbiol. (2001) 51:945-953.


External Information Resources (NCBI LinkOut)

LinkOut Subject LinkOut Provider
Archaea taxonomy/phylogenetic Encyclopedia of life
23 records from this provider organism-specific Integrated Microbial Genomes
Monera taxonomy/phylogenetic Integrated Taxonomic Information System
Archaea taxonomy/phylogenetic Lifemap
10 records from this provider taxonomy/phylogenetic NCBI taxonomy bookmarks
Archaea sp. (taxon passport) culture/stock collections StrainInfo
ToL taxonomy/phylogenetic Tree of Life
Archaea taxonomy/phylogenetic TreeBase
UCMP taxonomy/phylogenetic UCMP phylogeny exhibit
Archaea Woese, Kandler & Wheelis, 1990 taxonomy/phylogenetic World Register of Marine Species
Wikipedia taxonomy/phylogenetic iPhylo
Notes:
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