http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/new_micr.html


neighbors Archaea Genome Plasmids Bacteria Genome Plasmids Eukaryota Genome Plasmids Organelles Viruses

Viroids Plasmids Microbial Complete Genomes Taxonomy/List Archaea-16 Crenarchaeota Desulfurococcales-Aeropyrum pernix Sulfolobales-Sulfolobus

solfataricus-Sulfolobus tokodaii Thermoproteales-Pyrobaculum aerophilum Euryarchaeota Archaeoglobales-Archaeoglobus_fulgidus Halobacteriales-Halobacterium sp.

NRC-1 Methanobacteriales-Methanothermobacter thermautotrophicus Methanococcales-Methanococcus jannaschii Methanosarcinales-Methanosarcina acetivorans str.

C2a-Methanosarcina mazei Goe1 Methanopyrales-Methanopyrus kandleri AV19 Thermococcales-Pyrococcus abyssi-Pyrococcus

horikoshii-Pyrococcus_furiosus Thermoplasmales-Thermoplasma acidophilum-Thermoplasma volcanium Bacteria-64 Aquificales-Aquifex aeolicus Firmicutes

-Vibrio_cholerae delta/epsilon subdivisions-Campylobacter_jejuni-Helicobacter_pylori 26695-Helicobacter_pylori J99 Cyanobacteria Synechocystis PCC6803-Nostoc sp.


http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/eub_u.html


Submitting genome sequences All Organisms Prominent Organisms Microbial genomes BLAST List of projects Archaea Genome Plasmids unfinished Bacteria Genome

2213267 bp Nov 6 2001 Nitrosomonas europaea NC_002714 3007966 bp May 9 2002 Nostoc punctiforme NC_002791 8941326 bp May


http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/eub_g.html


Submitting genome sequences All Organisms Prominent Organisms Microbial genomes BLAST List of projects Archaea Genome Plasmids unfinished Bacteria Genome

Plasmids unfinished Eukaryota Genome Plasmids Organelles Viruses Phages Viroids Plasmids Bacteria Complete Genomes Taxonomy

2184406 bp Sep 27 2001 Nostoc sp. PCC 7120 NC_003272 6413771 bp Nov 28 2001 Pasteurella_multocida NC_002663 2257487 bp Sep


http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/new_eub_g.html


Prominent Organisms Microbial genomes BLAST List of projects Archaea Genome Plasmids Bacteria Genome Plasmids Eukaryota Genome

Plasmids Organelles Viruses Viroids Plasmids Bacteria genomes Taxonomy/List"40 Bacteria Aquificales-Aquifex


http://www.ncbi.nlm.nih.gov/Entrez/Genome/org.html


Taxonomy Tree BLAST List of projects PDB neighbors Archaea Genome Plasmids Bacteria Genome

1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Archaea-10 Crenarchaeota Euryarchaeota Aeropyrum pernix K1 Sulfolobus solfataricus Archaeoglobus_fulgidus Halobacterium sp. NRC

-1 Methanococcus jannaschii M. thermoautotrophicum Pyrococcus abyssi Pyrococcus horikoshii Thermoplasma acidophilum Thermoplasma volcanuim

Bacteria-41 Firmicutes Proteobacteria Bacillus_subtilis Bacillus halodurans C-125 Lactococcus_lactis Mycobacterium_leprae Mycobacterium_tuberculosis Mycobacterium_tuberculosis CDC1551


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik2?isbact=1


. trachomatis D. radiodurans E_coli K12 E_coli O157:

H7 E_coli O157:

Pyrococcus abyssi R. prowazekii R. solanacearum Rickettsia_conorii S. aureus subsp. aureus Mu50

C. pneumoniae CWL029 C. pneumoniae J138 C. trachomatis D. radiodurans E_coli K12

E_coli O157:

H7 E_coli O157:

Pyrococcus abyssi R. prowazekii R. solanacearum Rickettsia_conorii S. aureus subsp. aureus Mu50

C. pneumoniae CWL029 C. pneumoniae J138 C. trachomatis D. radiodurans E_coli K12

E_coli O157:

H7 E_coli O157:

Pyrococcus abyssi R. prowazekii R. solanacearum Rickettsia_conorii S. aureus subsp. aureus Mu50


http://www.ncbi.nlm.nih.gov/COG/


Code Name Proteins in COGS A Archaeoglobus_fulgidus 2420 1872 O Halobacterium sp.

NRC-1 2605 1701 M Methanococcus jannaschii 1786 1330 Methanobacterium thermoautotrophicum 1873 1388 P Thermoplasma acidophilum 1482 1230 Thermoplasma volcanium 1499 1243 K

Pyrococcus horikoshii 1800 1378 Pyrococcus abyssi 1768 1456 Z Aeropyrum pernix 1841 1178 Y Saccharomyces_cerevisiae 5955 2290 Q Aquifex aeolicus

7275 4959 Caulobacter_crescentus 3737 2628 X Rickettsia_prowazekii 835 697 I Chlamydia_trachomatis 895 631 Chlamydia_pneumoniae 1054 648 T Treponema_pallidum 1036 716 Borrelia_burgdorferi 1637 696 W Ureaplasma_urealyticum 614 406 Mycoplasma_pneumoniae 689 425 Mycoplasma


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=1488


pectinovorum'(Stormer) Beijerinck synonym Lineage (abbreviated) Bacteria;

Clostridia;

. and Jones, D. T.'Taxonomy and phylogeny of industrial solvent-producing clostridia.'


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=601


Bacillus typhi synonym, Bacterium (subgen.

,'Bacterium (subgen.

Eberthella) typhi'(Schroeter 1886) Buchanan 1918 synonym Lineage (abbreviated) Bacteria;

species of the Genus_salmonella Lignieres 1900 (approved lists 1980), rejection of the name Salmonella choleraesuis (Smith 1894) Weldin 1927 (approved lists 1980),

, pp. 1-814. No Pubmed record available. Buchanan RE (1918) Buchanan, R. E.'Studies in the nomenclature and classification of the bacteria. V


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=287


Pseudomonas_aeruginosa (Schroeter 1872) Migula 1900 synonym, Bacterium aeruginosum synonym,'Bacterium aeruginosum'Schroeter 1872 synonym,'Bacterium

1884) Flugge 1886 synonym, Pseudomonas pyocyanea synonym,'Pseudomonas pyocyanea'(Zopf 1884) Migula 1895 synonym, Bacterium pyocyaneum

synonym,'Bacterium pyocyaneum'(Zopf 1884) Lehmann and Neumann 1896 synonym, Pseudomonas polycolor synonym, probable synonym or variety:'

'Pseudomonas polycolor'Clara 1930 synonym Lineage (abbreviated) Bacteria;

. and Clark, W. A.'International code of nomenclature of bacteria (1990 revision).'


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=Genome&gi=167


Bacteria;

bacterium Bacillus halodurans and genomic sequence comparison with Bacillus_subtilis Takami, H.,Nakasone, K.,Takaki, Y


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=167


Bacteria;

bacterium Bacillus halodurans and genomic sequence comparison with Bacillus_subtilis Takami, H.,Nakasone, K.,Takaki, Y


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=103690


taxonomy id lock Taxonomy browser (Nostoc sp.

PCC 7120) Nostoc sp.

Nostoc sp.

strain PCC 7120 synonym, Nostoc (Anabaena) sp. PCC 7120 synonym, Anabaena PCC7120 synonym, Anabaena

ATCC 27893) synonym, Anabaena 7120 synonym, Nostoc PCC7120 synonym Lineage (abbreviated) Bacteria;

Nostocaceae;

Nostoc Nucleotide (157) Protein (12812) Structure (4) Genome records (7) Comments and questions to info@ncbi. nlm. nih.


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=813


trachomatis'(Busacca 1935) Moshkovski 1945 synonym Lineage (abbreviated) Bacteria;

revised taxonomy of the Family_chlamydiaceae, including a new genus and five new species,

. and Eiden, J. J.'Phylogenetic relationship of Chlamydia_pneumoniae to Chlamydia_psittaci and Chlamydia_trachomatis as determined by analysis of 16s ribosomal DNA sequences.'

. and Stephens, R. S.'Comparative genomes of Chlamydia_pneumoniae and C. trachomatis.'


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=86665


strain AH-101) includes Lineage (abbreviated) Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=139


Lyme_disease spirochete Rank:

. 1984 emend. Baranton et_al. 1992 synonym, Borrelia_burgdorferi sensu stricto equivalent name Lineage (abbreviated) Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c


Prokaryotes including the eubacteria (Kozak, 1983) and archaebacteria (Brown et_al.

CUG is_known to function as an initiator for_one plasmid-encoded protein (Repa) in Escherichia_coli (Spiers and Bergquist, 1992) and possibly in Methanobacterium thermoautotrophicum (Noelling et_al.

unpublished) There_is no record of AUU initition codon for the archaebacteria

. Evol. 28: 374-387 329-332. Medline Other Alternative Initiation Codons GUG, UUG (and possibly CUG) in the Archaea (Noelling et_al.

Other Alternative Initiation Codons GUG, UUG (and possibly CUG) in the Archaea (Noelling et_al.

phase dependent transcription of methane genes in two regions of the Methanobacterium thermoautotrophicum genome. Ohama,


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=305


Pseudomonas_solanacearum synonym, Burkholderia solanacearum synonym, Bacillus solanacearum synonym,'Bacillus solanacearum'synonym Lineage

(abbreviated) Bacteria;

. and Stead, D. E.'Names of plant pathogenic bacteria 1864-1995.'

. and Arakawa, M.'Proposal of Burkholderia gen. nov. and transfer of seven species of the Genus_pseudomonas homology group II to the new genus, with the type_species

1980)( Pseudomonas_solanacearum) Skerman, V. B. D.,Mcgowan, V,

and the blood_disease bacterium of banana based_on 16s rrna gene sequences.'


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=666


; Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=2107


. 1965 synonym Lineage (abbreviated) Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=180835


. C58 (Dupont) equivalent name Lineage (abbreviated) Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=115


Bacteria;

. This sequence was_determined by the E_coli Genome Project at the University of Wisconsin-Madison (Frederick R. Blattner, director.

The entire sequence was_determined independently from E_coli K-12 strain MG1655.

unique ID nos. for the genes in the E_coli Genetic Stock Center (CGSC) database at Yale_university, kindly supplied by Mary Berlyn. A public version

Updated information will_be available at the E_coli Genome Project's World_wide_web site (http://www. genetics. wisc.

***The E_coli K-12 sequence and its annotations are_updated periodically;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=1423


Bacteria;


http://www.ncbi.nlm.nih.gov:80/cgi-bin/Entrez/framik?db=Genome&gi=238


Bacteria;

. Mol. Microbiol. 21 (1), 77-96 (1996) 97000351 Complete genome sequence of the model actinomycete Streptomyces coelicolor A3 (2) Bentley, S_d.,Chater, K. F


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=90370


serovar Typhi synonym Lineage (abbreviated) Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=29459


Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=381


. 1982) Jarvis et_al. 1997 synonym, Rhizobium loti Jarvis et_al. 1982 synonym Lineage (abbreviated) Bacteria;

. and Patel, J. J.'Rhizobium loti, a new species of legume root nodule bacteria.'


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=Genome&gi=26


Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=85962


Helicobacter_pylori KE26695 synonym, Helicobacter_pylori ATCC700392 synonym, Helicobacter_pylori (strain 26695) synonym Lineage (abbreviated) Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=26


Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=113


Bacteria;

Mycoplasma. Complete sequence analysis of the genome of the bacterium Mycoplasma_pneumoniae Himmelreich, R.,Hilbert, H.,Plagens, H.,Pirkl


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=Genome&gi=176


Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=Genome&gi=113


Bacteria;

Mycoplasma. Complete sequence analysis of the genome of the bacterium Mycoplasma_pneumoniae Himmelreich, R.,Hilbert, H.,Plagens, H.,Pirkl


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=176


Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik?gi=204


(2596)- Listeriaceae (2596)- Bacillales (2522)- Bacilli (2469)- Bacillus/Clostridium group (2415)- Firmicutes (2394)- Bacteria (2063)- cellular organisms (738) 2846 Listeria_monocytogenes EGD-e proteins:

to change the blast threshold (cut_off) used to find related sequences Distribution of database hits Name Above cut_off Best Virus V 433 57 Eukaryota E 1664 20 Eubacteria

B 2561 2447 Archaea A 1602 22 Eubacteria+Archaea B A 2563 2469 Archaea+Eukaryota A_e 1964 42 Eukaryota+Eubacteria E B

2567 2467 Eukaryota+Eubacteria+Archaea E B A 2569 2489


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=1502


; Bacteria;

Clostridia;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik?gi=185


(3123)- Clostridiales (3122)- Clostridia (3088)- Bacillus/Clostridium group (2946)- Firmicutes (2931)- Bacteria (2635)- cellular organisms (1015) 3672 Clostridium acetobutylicum proteins:

to change the blast threshold (cut_off) used to find related sequences Distribution of database hits Name Above cut_off Best Virus V 664 23 Eukaryota E 2110 87 Eubacteria

B 3019 2590 Archaea A 2075 235 Eubacteria+Archaea B A 3050 2825 Archaea+Eukaryota A_e 2530 322 Eukaryota+Eubacteria E B

3067 2677 Eukaryota+Eubacteria+Archaea E B A 3094 2912


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=190650


. CB15 synonym Lineage (abbreviated) Bacteria;


http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome


Submitting genome sequences Prominent Organisms Microbial genomes Taxonomy Tree BLAST List of projects PDB neighbors Archaea

Genome Plasmids unfinshed Bacteria Genome Plasmids unfinshed Eukaryota Genome Plasmids Organelles Viruses

. All three main domains of life-bacteria

archaea, and eukaryota-are_represented,

Methanosarcina mazei strain Goe1 Publication Date:

. The Genome of Methanosarcina mazei:

Evidence for lateral gene transfer between Bacteria and Archaea.

4, 096,345 nt Methanosarcina mazei is an obligate anaerobic Archaea

. in rice_paddies. The genome sequencing of Methanosarcina mazei strain Goe1 has_been_completed


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=181661


. C58 (Cereon) synonym Lineage (abbreviated) Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=171101


Translation table 11 Lineage (abbreviated) Bacteria;

. and Glass, J. I.'The genome of the bacterium Streptococcus_pneumoniae strain R6.'


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=160490


Streptococcus_pyogenes (serotype 1/M1 GAS) synonym Lineage (abbreviated) Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=186103


Streptococcus_pyogenes (serotype 18/MGAS8232) synonym Lineage (abbreviated) Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=781


Rickettsia_conorii Brumpt 1932 synonym Lineage (abbreviated) Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=747


Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=Genome&gi=199


Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik?gi=128


subdivision (1226)- delta/epsilon subdivisions (1226)- Proteobacteria (1188)- Bacteria (1041)- cellular organisms (321) 1576 Helicobacter_pylori 26695 proteins:

to change the blast threshold (cut_off) used to find related sequences Distribution of database hits Name Above cut_off Best Virus V 207 9 Eukaryota E 871 39 Eubacteria

B 1258 1156 Archaea A 767 25 Eubacteria+Archaea B A 1264 1181 Archaea+Eukaryota A_e 1013 64 Eukaryota+Eubacteria E B

1282 1195 Eukaryota+Eubacteria+Archaea E B A 1287 1220


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik?gi=139


group (1283)- epsilon subdivision (1220)- delta/epsilon subdivisions (1220)- Proteobacteria (1187)- Bacteria (1033)- cellular organisms (312) 1491 Helicobacter_pylori J99 proteins:

to change the blast threshold (cut_off) used to find related sequences Distribution of database hits Name Above cut_off Best Virus V 198 7 Eukaryota E 868 43 Eubacteria

B 1248 1144 Archaea A 748 21 Eubacteria+Archaea B A 1255 1165 Archaea+Eukaryota A_e 1007 64 Eukaryota+Eubacteria E B

1271 1187 Eukaryota+Eubacteria+Archaea E B A 1277 1208


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik?gi=169


group (4512)- gamma subdivision (4348)- Proteobacteria (4140)- Bacteria (3634)- cellular organisms (1640) 5324 Escherichia_coli_o157:

to change the blast threshold (cut_off) used to find related sequences Distribution of database hits Name Above cut_off Best Virus V 1003 469 Eukaryota E 2641 103 Eubacteria

B 4202 3681 Archaea A 2328 41 Eubacteria+Archaea B A 4207 3722 Archaea+Eukaryota A_e 3085 144 Eukaryota+Eubacteria E B

4251 3784 Eukaryota+Eubacteria+Archaea E B A 4255 3825


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik?gi=221


(1665)- Rhizobiaceae group (1633)- alpha subdivision (1622)- Proteobacteria (1548)- Bacteria (1392)- cellular organisms (522) 1876 Agrobacterium_tumefaciens str.

to change the blast threshold (cut_off) used to find related sequences Distribution of database hits Name Above cut_off Best Virus V 246 0 Eukaryota E 1137 9 Eubacteria

B 1660 1602 Archaea A 1190 22 Eubacteria+Archaea B A 1661 1624 Archaea+Eukaryota A_e 1355 31 Eukaryota+Eubacteria E B

1662 1611 Eukaryota+Eubacteria+Archaea E B A 1663 1633


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=199


Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik?gi=189


group (2363)- alpha subdivision (2304)- Proteobacteria (2199)- Bacteria (1933)- cellular organisms (619) 2721 Agrobacterium_tumefaciens str.

to change the blast threshold (cut_off) used to find related sequences Distribution of database hits Name Above cut_off Best Virus V 316 3 Eukaryota E 1594 14 Eubacteria

B 2470 2426 Archaea A 1482 11 Eubacteria+Archaea B A 2471 2437 Archaea+Eukaryota A_e 1870 25 Eukaryota+Eubacteria E B

2471 2440 Eukaryota+Eubacteria+Archaea E B A 2472 2451


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik?gi=220


(2453)- Rhizobiaceae group (2358)- alpha subdivision (2305)- Proteobacteria (2206)- Bacteria (1942)- cellular organisms (615) 2785 Agrobacterium_tumefaciens str.

to change the blast threshold (cut_off) used to find related sequences Distribution of database hits Name Above cut_off Best Virus V 311 3 Eukaryota E 1600 15 Eubacteria

B 2448 2406 Archaea A 1489 10 Eubacteria+Archaea B A 2450 2416 Archaea+Eukaryota A_e 1883 25 Eukaryota+Eubacteria E B

2449 2421 Eukaryota+Eubacteria+Archaea E B A 2451 2431


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik?gi=190


group (1635)- alpha subdivision (1622)- Proteobacteria (1543)- Bacteria (1388)- cellular organisms (519) 1833 Agrobacterium_tumefaciens str.

to change the blast threshold (cut_off) used to find related sequences Distribution of database hits Name Above cut_off Best Virus V 248 0 Eukaryota E 1135 12 Eubacteria

B 1665 1605 Archaea A 1186 22 Eubacteria+Archaea B A 1666 1627 Archaea+Eukaryota A_e 1354 34 Eukaryota+Eubacteria E B

1668 1617 Eukaryota+Eubacteria+Archaea E B A 1669 1639


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik?gi=177


group (3243)- alpha subdivision (3124)- Proteobacteria (2947)- Bacteria (2533)- cellular organisms (796) 3737 Caulobacter_crescentus CB15 proteins:

to change the blast threshold (cut_off) used to find related sequences Distribution of database hits Name Above cut_off Best Virus V 405 8 Eukaryota E 2140 71 Eubacteria

B 3195 3038 Archaea A 1807 34 Eubacteria+Archaea B A 3200 3072 Archaea+Eukaryota A_e 2443 105 Eukaryota+Eubacteria E B

3229 3109 Eukaryota+Eubacteria+Archaea E B A 3232 3143


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik?gi=160


(767)- Chlamydiales/Verrucomicrobia group (767)- Bacteria (666)- cellular organisms (204) 1069 Chlamydophila_pneumoniae J138 proteins:

to change the blast threshold (cut_off) used to find related sequences Distribution of database hits Name Above cut_off Best Virus V 126 3 Eukaryota E 594 88 Eubacteria

B 732 584 Archaea A 468 27 Eubacteria+Archaea B A 737 611 Archaea+Eukaryota A_e 651 115 Eukaryota+Eubacteria E B

756 672 Eukaryota+Eubacteria+Archaea E B A 760 699


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik?gi=115


group (3827)- gamma subdivision (3674)- Proteobacteria (3484)- Bacteria (3061)- cellular organisms (1108) 4279 Escherichia_coli K12 proteins:

to change the blast threshold (cut_off) used to find related sequences Distribution of database hits Name Above cut_off Best Virus V 523 93 Eukaryota E 2484 102 Eubacteria

B 3754 3400 Archaea A 2238 43 Eubacteria+Archaea B A 3759 3443 Archaea+Eukaryota A_e 2884 145 Eukaryota+Eubacteria E B

3774 3502 Eukaryota+Eubacteria+Archaea E B A 3778 3545


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik?gi=164


and aphid endosymbionts (564)- Enterobacteriaceae group (562)- gamma subdivision (558)- Proteobacteria (546)- Bacteria (508)- cellular organisms (154) 564 Buchnera sp.

to change the blast threshold (cut_off) used to find related sequences Distribution of database hits Name Above cut_off Best Virus V 94 0 Eukaryota E 481 4 Eubacteria

B 562 553 Archaea A 361 0 Eubacteria+Archaea B A 562 553 Archaea+Eukaryota A_e 502 4 Eukaryota+Eubacteria E B

564 557 Eukaryota+Eubacteria+Archaea E B A 564 557


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik?gi=167


Bacillus halodurans Taxtable BLAST Pubmed Nucleotide Protein Genome Structure Taxonomy-Bacillales (3361)- Bacilli

(3331)- Bacillus/Clostridium group (3188)- Firmicutes (3166)- Bacteria (2789)- cellular organisms (1022) 4066 Bacillus halodurans proteins:

to change the blast threshold (cut_off) used to find related sequences Distribution of database hits Name Above cut_off Best Virus V 502 50 Eukaryota E 2156 80 Eubacteria

B 3293 2877 Archaea A 2281 194 Eubacteria+Archaea B A 3317 3071 Archaea+Eukaryota A_e 2712 274 Eukaryota+Eubacteria E B

3325 2957 Eukaryota+Eubacteria+Archaea E B A 3345 3151


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik?gi=27


Bacillus_subtilis Taxtable BLAST Pubmed Nucleotide Protein Genome Structure Taxonomy-Bacillales (3510)- Bacilli (3474)- Bacillus

/Clostridium group (3351)- Firmicutes (3327)- Bacteria (2983)- cellular organisms (1216) 4112 Bacillus_subtilis proteins:

to change the blast threshold (cut_off) used to find related sequences Distribution of database hits Name Above cut_off Best Virus V 683 272 Eukaryota E 2259 67 Eubacteria

B 3292 2848 Archaea A 2272 174 Eubacteria+Archaea B A 3318 3022 Archaea+Eukaryota A_e 2715 241 Eukaryota+Eubacteria E B

3323 2915 Eukaryota+Eubacteria+Archaea E B A 3346 3089


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=25


Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=2104


Lineage (abbreviated) Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=1642


innocua Seeliger 1983 misnomer Lineage (abbreviated) Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=83560


. 1999 synonym, agent of mouse pneumonitis common name Lineage (abbreviated) Bacteria;

revised taxonomy of the Family_chlamydiaceae, including a new genus and five new species,


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=115713


Chlamydia_pneumoniae CWL029 synonym Lineage (abbreviated) Bacteria;

. and Nakazawa, T.'Comparison of whole genome sequences of Chlamydia_pneumoniae J138 from Japan andcwl029 from USA.'

. and Stephens, R. S.'Comparative genomes of Chlamydia_pneumoniae and C. trachomatis.'


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=Genome&gi=25


Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=2097


. 1983 synonym Lineage (abbreviated) Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=115711


Chlamydia_pneumoniae AR39 synonym Lineage (abbreviated) Bacteria;

. and Fraser, C. M.'Genome sequences of Chlamydia_trachomatis Mopn and Chlamydia_pneumoniae AR39.'


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=1769


, Mycoplasma leprae misnomer Lineage (abbreviated) Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=170187


Translation table 11 Lineage (abbreviated) Bacteria;


http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?id=1360


Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=Genome&gi=188


Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=Genome&gi=179


Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=Genome&gi=182


Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=Genome&gi=198


Bacteria;

Streptococcus. Genome of the bacterium Streptococcus_pneumoniae strain R6 Hoskins, J. A.,Alborn, W. Jr.


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=Genome&gi=13170


Bacteria;

Borrelia_burgdorferi_group. Genomic sequence of a Lyme_disease spirochaete, Borrelia_burgdorferi Fraser, C. M.,Casjens, S.,Huang, W


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=Genome&gi=13171


Bacteria;

Borrelia_burgdorferi_group. Genomic sequence of a Lyme_disease spirochaete, Borrelia_burgdorferi Fraser, C. M.,Casjens, S.,Huang, W


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=Genome&gi=205


Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=204


Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=183


Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=171


Bacteria;

Lactococcus. The complete genome sequence of the lactic_acid bacterium Lactococcus_lactis ssp. lactis IL1403 Bolotin, A.,Wincker, P.,Mauger


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=179


Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=182


Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=198


Bacteria;

Streptococcus. Genome of the bacterium Streptococcus_pneumoniae strain R6 Hoskins, J. A.,Alborn, W. Jr.


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=27


Bacteria;

Bacillus. The complete genome sequence of the gram-positive bacterium Bacillus_subtilis Kunst, F.,Ogasawara, N.,Moszer, I.,Albertini, A_m.,Alloni


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/taxik?gi=25


group (1641)- gamma subdivision (1571)- Proteobacteria (1490)- Bacteria (1305)- cellular organisms (413) 1714 Haemophilus_influenzae Rd proteins:

to change the blast threshold (cut_off) used to find related sequences Distribution of database hits Name Above cut_off Best Virus V 237 24 Eukaryota E 1086 8 Eubacteria

B 1635 1570 Archaea A 957 9 Eubacteria+Archaea B A 1636 1579 Archaea+Eukaryota A_e 1244 17 Eukaryota+Eubacteria E B

1636 1578 Eukaryota+Eubacteria+Archaea E B A 1637 1587


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=151


Bacteria;


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=Genome&gi=14097


Bacteria;

Clostridia;

Clostridium. Genome Sequence and Comparative Analysis of the Solvent-Producing Bacterium Clostridium acetobutylicum Nolling, J.,Breton


http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=205


Bacteria;


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