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Home , Acholeplasmataceae, Actinobacteridae, Cellulomonadaceae, Desulfurococcales, Halobacteriaceae, Methanococcaceae

Table S1. Taxonomic distribution of the trmA and trmFO (gid ) genes coding for putative tRNA:m5U-54 methyltransferases in 355 bacterial and archaeal complete genomes. Asterisks indicate the presence and the number of putative genes found. Genomes Taxonomic position TrmA Gid Crenarchaea pernix_K1 ; ; ; Cenarchaeum symbiosum Crenarchaeota; Thermoprotei; ; Cenarchaeaceae aerophilum_str_IM2 Crenarchaeota; Thermoprotei; ; acidocaldarius_DSM_639 Crenarchaeota; Thermoprotei; ; Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Euryarchaea Archaeoglobus fulgidus ; Archaeoglobi; Archaeoglobales; marismortui_ATCC_43049 Euryarchaeota; Halobacteria; ; ; Haloarcula sp Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula walsbyi Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloquadra Methanobacterium thermoautotrophicum Euryarchaeota; ; ; Methanobacteriaceae burtonii_DSM_6242 Euryarchaeota; ; ; jannaschii Euryarchaeota; ; ; Methanococcaceae Methanococcus maripaludis_S2 Euryarchaeota; Methanococci; Methanococcales; Methanococcaceae kandleri Euryarchaeota; ; ; acetivorans Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae Methanosarcina barkeri_fusaro Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae Methanosarcina mazei Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae Methanosphaera stadtmanae Euryarchaeota; Methanobacteria; Methanobacteriales; Methanobacteriaceae hungatei_JF_1 Euryarchaeota; Methanomicrobia; ; Methanospirillaceae pharaonis Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Natronomonas torridus_DSM_9790 Euryarchaeota; ; ; Picrophilaceae Pyrococcus abyssi Euryarchaeota; ; ; Thermococcaceae Pyrococcus furiosus Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae Pyrococcus horikoshii Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae Thermococcus kodakaraensis_KOD1 Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae acidophilum Euryarchaeota; Thermoplasmata; Thermoplasmatales; Thermoplasmataceae Euryarchaeota; Thermoplasmata; Thermoplasmatales; Thermoplasmataceae Nanoarchaea Nanoarchaeum equitans Acidobacteria bacterium_Ellin345 /Acidobacteria group * Bifidobacterium longum Actinobacteria; Actinobacteria (class); ; Bifidobacteriales; diphtheriae Actinobacteria; Actinobacteria (class); Actinobacteridae; ; Corynebacterineae; Corynebacteriaceae Corynebacterium efficiens_YS_314 Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Corynebacteriaceae Corynebacterium glutamicum_ATCC_13032_K Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Corynebacteriaceae Corynebacterium glutamicum_ATCC_13032_K Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Corynebacteriaceae Corynebacterium jeikeium_K411 Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Corynebacteriaceae CcI3 Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Frankineae; Frankiaceae Leifsonia xyli_xyli_CTCB0 Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Micrococcineae; Microbacteriaceae avium Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae

urbonavicus_MIE_2007_tableS1.xls 1 01/02/2007 Mycobacterium MCS Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae Mycobacterium tuberculosis_CDC1551 Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae Mycobacterium tuberculosis_H37Rv Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Mycobacteriaceae farcinica_IFM10152 Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Corynebacterineae; Propionibacterium acnes_KPA171202 Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Propionibacterineae; Rubrobacter xylanophilus_DSM_9941 Actinobacteria; Actinobacteria (class); Rubrobacteridae; Rubrobacterales; Rubrobacterineae; Rubrobacteraceae * avermitilis Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Streptomycineae; Streptomyces coelicolor Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Streptomycineae; Streptomycetaceae Thermobifida fusca_YX Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Streptosporangineae; Nocardiopsaceae Tropheryma whipplei_TW08_27 Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Micrococcineae; Cellulomonadaceae Tropheryma whipplei_Twist Actinobacteria; Actinobacteria (class); Actinobacteridae; Actinomycetales; Micrococcineae; Cellulomonadaceae Aquifex aeolicus Aquificae; Aquificae (class); Aquificales; Aquificaceae * Bacteroides fragilis_NCTC_9434 Bacteroidetes/Chlorobi group; Bacteroidetes; Bacteroidetes (class); Bacteroidales; Bacteroidaceae Bacteroides fragilis_YCH46 Bacteroidetes/Chlorobi group; Bacteroidetes; Bacteroidetes (class); Bacteroidales; Bacteroidaceae Bacteroides thetaiotaomicron_VPI_5482 Bacteroidetes/Chlorobi group; Bacteroidetes; Bacteroidetes (class); Bacteroidales; Bacteroidaceae Chlorobium chlorochromatii_CaD3 Bacteroidetes/Chlorobi group; Chlorobi; Chlorobia; Chlorobiales; Chlorobiaceae; Chlorobium/Pelodictyon group Chlorobium tepidum_TLS Bacteroidetes/Chlorobi group; Chlorobi; Chlorobia; Chlorobiales; Chlorobiaceae; Chlorobium/Pelodictyon group Pelodictyon luteolum_DSM_273 Bacteroidetes/Chlorobi group; Chlorobi; Chlorobia; Chlorobiales; Chlorobiaceae; Chlorobium/Pelodictyon group Porphyromonas gingivalis_W83 Bacteroidetes/Chlorobi group; Bacteroidetes; Bacteroidetes (class); Bacteroidales; Porphyromonadaceae Salinibacter ruber_DSM_13855 Bacteroidetes/Chlorobi group; Bacteroidetes; ; Sphingobacteriales; Crenotrichaceae PVC group Chlamydia muridarum / group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydia trachomatis Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydia trachomatis_A_HAR_13 Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydophila abortus_S26_3 Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydophila caviae Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydophila felis_Fe_C_56 Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydophila pneumoniae_AR39 Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydophila pneumoniae_CWL029 Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydophila pneumoniae_J138 Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Chlamydophila pneumoniae_TW_183 Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Chlamydiaceae Protochlamydia amoebophila UWE25 Chlamydiae/Verrucomicrobia group; Chlamydiae; Chlamydiae (class); Chlamydiales; Parachlamydiaceae Rhodopirellula baltica SH1 ; Planctomycetacia; Planctomycetales; Planctomycetaceae; Rhodopirellula Dehalococcoides CBDB1 Chloroflexi; Dehalococcoidetes Dehalococcoides ethenogenes_195 Chloroflexi; Dehalococcoidetes Anabaena variabilis_ATCC_29413 Cyanobacteria; Nostocales; Nostocaceae * Gloeobacter violaceus Cyanobacteria; Gloeobacteria; Gloeobacterales * Nostoc sp Cyanobacteria; Nostocales; Nostocaceae * Prochlorococcus marinus_CCMP1375 Cyanobacteria; Prochlorales; Prochlorococcaceae * Prochlorococcus marinus_MED4 Cyanobacteria; Prochlorales; Prochlorococcaceae * Prochlorococcus marinus_MIT_9312 Cyanobacteria; Prochlorales; Prochlorococcaceae * Prochlorococcus marinus_MIT9313 Cyanobacteria; Prochlorales; Prochlorococcaceae * Prochlorococcus marinus_NATL2A Cyanobacteria; Prochlorales; Prochlorococcaceae * Synechococcus CC9605 Cyanobacteria; Chroococcales * Synechococcus CC9902 Cyanobacteria; Chroococcales * Synechococcus elongatus_PCC_6301 Cyanobacteria; Chroococcales * Synechococcus elongatus_PCC_7942 Cyanobacteria; Chroococcales *

urbonavicus_MIE_2007_tableS1.xls 2 01/02/2007 Synechococcus sp. JA-2-3B'a (Cyanobacteria Yellowstone B-Prime) Cyanobacteria; Chroococcales * Synechococcus sp. JA-3-3Ab (Cyanobacteria Yellowstone A-Prime) Cyanobacteria; Chroococcales * Synechococcus sp_WH8102 Cyanobacteria; Chroococcales * Synechocystis PCC6803 Cyanobacteria; Chroococcales * Thermosynechococcus elongatus Cyanobacteria; Chroococcales * Deinococci Deinococcus geothermalis_DSM_11300 Deinococcus-Thermus; Deinococci; Deinococcales; Deinococcaceae * Deinococcus radiodurans Deinococcus-Thermus; Deinococci; Deinococcales; Deinococcaceae * Thermus thermophilus_HB27 Deinococcus-Thermus; Deinococci; Thermales; Thermaceae * Thermus thermophilus_HB8 Deinococcus-Thermus; Deinococci; Thermales; Thermaceae * Aster yellows_witches_broom_phytoplasma Firmicutes; ; Acholeplasmatales; Acholeplasmataceae anthracis_Ames Firmicutes; ; Bacillales; Bacillaceae * Bacillus anthracis_str. 'Ames Ancestor' Firmicutes; Bacilli; Bacillales; Bacillaceae * Bacillus anthracis_str_Sterne Firmicutes; Bacilli; Bacillales; Bacillaceae * Bacillus cereus_ATCC10987 Firmicutes; Bacilli; Bacillales; Bacillaceae * Bacillus cereus_ATCC14579 Firmicutes; Bacilli; Bacillales; Bacillaceae * Bacillus cereus_E33L Firmicutes; Bacilli; Bacillales; Bacillaceae * Bacillus clausii_KSM_K16 Firmicutes; Bacilli; Bacillales; Bacillaceae * Bacillus halodurans Firmicutes; Bacilli; Bacillales; Bacillaceae * Bacillus licheniformis_ATCC_14580 Firmicutes; Bacilli; Bacillales; Bacillaceae * Bacillus licheniformis_DSM_13 Firmicutes; Bacilli; Bacillales; Bacillaceae * Bacillus subtilis Firmicutes; Bacilli; Bacillales; Bacillaceae * Bacillus thuringiensis_konkukian Firmicutes; Bacilli; Bacillales; Bacillaceae * Carboxydothermus hydrogenoformans_Z_290 Firmicutes; Clostridia; Clostridiales; Peptococcaceae * Clostridium acetobutylicum Firmicutes; Clostridia; Clostridiales; Clostridiaceae Clostridium perfringens Firmicutes; Clostridia; Clostridiales; Clostridiaceae Clostridium tetani_E88 Firmicutes; Clostridia; Clostridiales; Clostridiaceae Desulfitobacterium hafniense_Y51 Firmicutes; Clostridia; Clostridiales; Peptococcaceae * Enterococcus faecalis_V583 Firmicutes; Bacilli; Lactobacillales; Enterococcaceae * Geobacillus kaustophilus_HTA426 Firmicutes; Bacilli; Bacillales; Bacillaceae Lactobacillus acidophilus_NCFM Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae * Lactobacillus delbrueckii_bulgaricus Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae * Lactobacillus johnsonii_NCC_533 Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae * Lactobacillus plantarum Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae * Lactobacillus sakei_23K Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae ** Lactobacillus salivarius_UCC118 Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae * Lactococcus lactis Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae * Listeria innocua Firmicutes; Bacilli; Bacillales; Listeriaceae * Listeria monocytogenes Firmicutes; Bacilli; Bacillales; Listeriaceae * Listeria monocytogenes_4b_F2365 Firmicutes; Bacilli; Bacillales; Listeriaceae * Mesoplasma florum_L1 Firmicutes; Mollicutes; Entomoplasmatales; Entomoplasmataceae ** Moorella thermoacetica_ATCC_39073 Firmicutes; Clostridia; Thermoanaerobacteriales; Thermoanaerobacteriaceae; Moorella group * Mycoplasma capricolum_ATCC_27343 Firmicutes; Mollicutes; Mycoplasmatales; ** Mycoplasma gallisepticum Firmicutes; Mollicutes; Mycoplasmatales; Mycoplasmataceae Mycoplasma genitalium Firmicutes; Mollicutes; Mycoplasmatales; Mycoplasmataceae Mycoplasma hyopneumoniae_232 Firmicutes; Mollicutes; Mycoplasmatales; Mycoplasmataceae Mycoplasma hyopneumoniae_7448 Firmicutes; Mollicutes; Mycoplasmatales; Mycoplasmataceae Mycoplasma hyopneumoniae_J Firmicutes; Mollicutes; Mycoplasmatales; Mycoplasmataceae Mycoplasma mobile_163K Firmicutes; Mollicutes; Mycoplasmatales; Mycoplasmataceae Mycoplasma mycoides Firmicutes; Mollicutes; Mycoplasmatales; Mycoplasmataceae **

urbonavicus_MIE_2007_tableS1.xls 3 01/02/2007 Mycoplasma penetrans Firmicutes; Mollicutes; Mycoplasmatales; Mycoplasmataceae Mycoplasma pneumoniae Firmicutes; Mollicutes; Mycoplasmatales; Mycoplasmataceae Mycoplasma pulmonis Firmicutes; Mollicutes; Mycoplasmatales; Mycoplasmataceae Mycoplasma synoviae_53 Firmicutes; Mollicutes; Mycoplasmatales; Mycoplasmataceae Oceanobacillus iheyensis Firmicutes; Bacilli; Bacillales; Bacillaceae Onion yellows_phytoplasma Firmicutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae Staphylococcus aureus_aureus_MRSA252 Firmicutes; Bacilli; Bacillales; Staphylococcaceae * Staphylococcus aureus_aureus_MSSA476 Firmicutes; Bacilli; Bacillales; Staphylococcaceae * Staphylococcus aureus_COL Firmicutes; Bacilli; Bacillales; Staphylococcaceae * Staphylococcus aureus_Mu50 Firmicutes; Bacilli; Bacillales; Staphylococcaceae * Staphylococcus aureus_MW2 Firmicutes; Bacilli; Bacillales; Staphylococcaceae * Staphylococcus aureus_N315 Firmicutes; Bacilli; Bacillales; Staphylococcaceae * Staphylococcus aureus_NCTC_8325 Firmicutes; Bacilli; Bacillales; Staphylococcaceae * Staphylococcus aureus_RF122 Firmicutes; Bacilli; Bacillales; Staphylococcaceae * Staphylococcus aureus_USA300 Firmicutes; Bacilli; Bacillales; Staphylococcaceae * Staphylococcus epidermidis_ATCC_12228 Firmicutes; Bacilli; Bacillales; Staphylococcaceae * Staphylococcus epidermidis_RP62A Firmicutes; Bacilli; Bacillales; Staphylococcaceae * Staphylococcus haemolyticus Firmicutes; Bacilli; Bacillales; Staphylococcaceae * Staphylococcus saprophyticus Firmicutes; Bacilli; Bacillales; Staphylococcaceae * Streptococcus agalactiae_2603 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus agalactiae_A909 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus agalactiae_NEM316 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus mutans Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus pneumoniae_R6 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus pneumoniae_TIGR4 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus pyogenes_M1_GAS Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus pyogenes_MGAS10270 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus pyogenes_MGAS10394 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus pyogenes_MGAS10750 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus pyogenes_MGAS2096 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus pyogenes_MGAS315 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus pyogenes_MGAS5005 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus pyogenes_MGAS6180 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus pyogenes_MGAS8232 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus pyogenes_MGAS9429 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus pyogenes_SSI_1 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus thermophilus_CNRZ1066 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Streptococcus thermophilus_LMG_18311 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae * Symbiobacterium thermophilum_IAM14863 Firmicutes * Thermoanaerobacter tengcongensis Firmicutes; Clostridia; Thermoanaerobacteriales; Thermoanaerobacteriaceae Ureaplasma urealyticum Firmicutes; Mollicutes; Mycoplasmatales; Mycoplasmataceae Fusobacterium nucleatum Fusobacteria; Fusobacteria (class); Fusobacterales; Fusobacteriaceae * Alphaproteobacteria Agrobacterium tumefaciens_C58_Cereon ; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium * Agrobacterium tumefaciens_C58_UWash Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium * Anaplasma marginale_St_Maries Proteobacteria; Alphaproteobacteria; Rickettsiales; Anaplasmataceae Anaplasma phagocytophilum_HZ Proteobacteria; Alphaproteobacteria; Rickettsiales; Anaplasmataceae Bartonella henselae_Houston_1 Proteobacteria; Alphaproteobacteria; Rhizobiales; Bartonellaceae; Bartonella * Bartonella quintana_Toulouse Proteobacteria; Alphaproteobacteria; Rhizobiales; Bartonellaceae; Bartonella Bradyrhizobium japonicum Proteobacteria; Alphaproteobacteria; Rhizobiales; Bradyrhizobiaceae; Bradyrhizobium *

urbonavicus_MIE_2007_tableS1.xls 4 01/02/2007 Brucella abortus_9_941 Proteobacteria; Alphaproteobacteria; Rhizobiales; Brucellaceae * Brucella melitensis Proteobacteria; Alphaproteobacteria; Rhizobiales; Brucellaceae * Brucella melitensis_biovar_Abortus Proteobacteria; Alphaproteobacteria; Rhizobiales; Brucellaceae * Brucella suis_1330 Proteobacteria; Alphaproteobacteria; Rhizobiales; Brucellaceae * Candidatus Pelagibacter_ubique_HTCC1062 Proteobacteria; Alphaproteobacteria; Rickettsiales; SAR11 cluster Caulobacter crescentus Proteobacteria; Alphaproteobacteria; Caulobacterales; Caulobacteraceae * Ehrlichia canis_Jake Proteobacteria; Alphaproteobacteria; Rickettsiales; Anaplasmataceae; Ehrlichia Ehrlichia chaffeensis_Arkansas Proteobacteria; Alphaproteobacteria; Rickettsiales; Anaplasmataceae; Ehrlichia Ehrlichia ruminantium_Gardel Proteobacteria; Alphaproteobacteria; Rickettsiales; Anaplasmataceae; Ehrlichia Ehrlichia ruminantium_str._Welgevonden Proteobacteria; Alphaproteobacteria; Rickettsiales; Anaplasmataceae; Ehrlichia Ehrlichia ruminantium_Welgevonden Proteobacteria; Alphaproteobacteria; Rickettsiales; Anaplasmataceae; Ehrlichia Erythrobacter litoralis_HTCC2594 Proteobacteria; Alphaproteobacteria; Sphingomonadales; Erythrobacteraceae * Gluconobacter oxydans_621H Proteobacteria; Alphaproteobacteria; Rhodospirillales; Acetobacteraceae Jannaschia CCS1 Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae * Magnetospirillum magneticum_AMB_1 Proteobacteria; Alphaproteobacteria; Rhodospirillales; Rhodospirillaceae * Mesorhizobium loti Proteobacteria; Alphaproteobacteria; Rhizobiales; Phyllobacteriaceae * Neorickettsia sennetsu_Miyayama Proteobacteria; Alphaproteobacteria; Rickettsiales; Anaplasmataceae Nitrobacter hamburgensis_X14 Proteobacteria; Alphaproteobacteria; Rhizobiales; Bradyrhizobiaceae * Nitrobacter winogradskyi_Nb_255 Proteobacteria; Alphaproteobacteria; Rhizobiales; Bradyrhizobiaceae * Novosphingobium aromaticivorans_DSM_124 Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae * Rhizobium etli_CFN_42 Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Rhizobium/Agrobacterium group * Rhodobacter sphaeroides_2_4_1 Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae * Rhodopseudomonas palustris_BisB18 Proteobacteria; Alphaproteobacteria; Rhizobiales; Bradyrhizobiaceae * Rhodopseudomonas palustris_BisB5 Proteobacteria; Alphaproteobacteria; Rhizobiales; Bradyrhizobiaceae * Rhodopseudomonas palustris_CGA009 Proteobacteria; Alphaproteobacteria; Rhizobiales; Bradyrhizobiaceae * Rhodopseudomonas palustris_HaA2 Proteobacteria; Alphaproteobacteria; Rhizobiales; Bradyrhizobiaceae * Rhodospirillum rubrum_ATCC_11170 Proteobacteria; Alphaproteobacteria; Rhodospirillales; Rhodospirillaceae * Rickettsia bellii_RML369_C Proteobacteria; Alphaproteobacteria; Rickettsiales; Rickettsiaceae; Rickettsieae; Rickettsia Rickettsia conorii Proteobacteria; Alphaproteobacteria; Rickettsiales; Rickettsiaceae; Rickettsieae; Rickettsia Rickettsia felis_URRWXCal2 Proteobacteria; Alphaproteobacteria; Rickettsiales; Rickettsiaceae; Rickettsieae; Rickettsia Rickettsia prowazekii Proteobacteria; Alphaproteobacteria; Rickettsiales; Rickettsiaceae; Rickettsieae; Rickettsia Rickettsia typhi_wilmington Proteobacteria; Alphaproteobacteria; Rickettsiales; Rickettsiaceae; Rickettsieae; Rickettsia Silicibacter pomeroyi_DSS3 Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae * Silicibacter TM1040 Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae * Sinorhizobium meliloti Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae; Sinorhizobium/Ensifer group * Sphingopyxis alaskensis_RB2256 Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae * Wolbachia endosymbiont_of_Brugia_malayi Proteobacteria; Alphaproteobacteria; Rickettsiales; Rickettsiaceae; Wolbachieae Wolbachia endosymbiont_of_Drosophila_me Proteobacteria; Alphaproteobacteria; Rickettsiales; Rickettsiaceae; Wolbachieae Zymomonas mobilis_ZM4 Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Zymomonas * Betaproteobacteria Azoarcus sp_EbN1 Proteobacteria; Betaproteobacteria; Rhodocyclales; Rhodocyclaceae * Bordetella bronchiseptica Proteobacteria; Betaproteobacteria; Burkholderiales; Alcaligenaceae Bordetella parapertussis Proteobacteria; Betaproteobacteria; Burkholderiales; Alcaligenaceae Bordetella pertussis Proteobacteria; Betaproteobacteria; Burkholderiales; Alcaligenaceae Burkholderia 383 Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae Burkholderia cenocepacia_AU_1054 Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae Burkholderia mallei_ATCC_23344 Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae Burkholderia pseudomallei_1710b Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae Burkholderia pseudomallei_K96243 Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae Burkholderia thailandensis_E264 Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae Burkholderia xenovorans_LB400 Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae

urbonavicus_MIE_2007_tableS1.xls 5 01/02/2007 Chromobacterium violaceum Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae; Chromobacterium group Dechloromonas aromatica_RCB Proteobacteria; Betaproteobacteria; Rhodocyclales; Rhodocyclaceae * Methylobacillus flagellatus_KT Proteobacteria; Betaproteobacteria; Methylophilales; Methylophilaceae Neisseria gonorrhoeae_FA_1090 Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae; Neisseria * Neisseria meningitidis_MC58 Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae; Neisseria * Neisseria meningitidis_Z2491 Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae; Neisseria * Nitrosomonas europaea Proteobacteria; Betaproteobacteria; Nitrosomonadales; Nitrosomonadaceae Nitrosospira multiformis_ATCC_25196 Proteobacteria; Betaproteobacteria; Nitrosomonadales; Nitrosomonadaceae Polaromonas JS666 Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae Ralstonia eutropha_JMP134 Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae Ralstonia metallidurans_CH34 Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae Ralstonia solanacearum Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae Rhodoferax ferrireducens_T118 Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae Thiobacillus denitrificans_ATCC_25259 Proteobacteria; Betaproteobacteria; Hydrogenophilales; Hydrogenophilaceae Deltaproteobacteria Anaeromyxobacter dehalogenans_2CP_C Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Myxococcales; Cystobacterineae; Myxococcaceae * Bdellovibrio bacteriovorus Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Bdellovibrionales; Bdellovibrionaceae * Desulfotalea psychrophila_LSv54 Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfobacterales; Desulfobulbaceae * Desulfovibrio desulfuricans_G20 Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfovibrionales; Desulfovibrionaceae * Desulfovibrio vulgaris_Hildenborough Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfovibrionales; Desulfovibrionaceae * Geobacter metallireducens_GS_15 Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfuromonadales; Geobacteraceae * Geobacter sulfurreducens Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfuromonadales; Geobacteraceae * Lawsonia intracellularis_PHE_MN1_00 Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfovibrionales; Desulfovibrionaceae * Myxococcus xanthus_DK_1622 Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Myxococcales; Cystobacterineae; Myxococcaceae * Pelobacter carbinolicus Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Desulfuromonadales; Pelobacteraceae * Syntrophus aciditrophicus_SB Proteobacteria; delta/epsilon subdivisions; Deltaproteobacteria; Syntrophobacterales; Syntrophaceae * Epsilonproteobacteria Campylobacter jejuni Proteobacteria; delta/epsilon subdivisions; Epsilonproteobacteria; Campylobacterales; Campylobacteraceae * Campylobacter jejuni_RM1221 Proteobacteria; delta/epsilon subdivisions; Epsilonproteobacteria; Campylobacterales; Campylobacteraceae * Helicobacter acinonychis_Sheeba Proteobacteria; delta/epsilon subdivisions; Epsilonproteobacteria; Campylobacterales; Helicobacteraceae Helicobacter hepaticus Proteobacteria; delta/epsilon subdivisions; Epsilonproteobacteria; Campylobacterales; Helicobacteraceae * Helicobacter pylori_26695 Proteobacteria; delta/epsilon subdivisions; Epsilonproteobacteria; Campylobacterales; Helicobacteraceae Helicobacter pylori_HPAG1 Proteobacteria; delta/epsilon subdivisions; Epsilonproteobacteria; Campylobacterales; Helicobacteraceae Helicobacter pylori_J99 Proteobacteria; delta/epsilon subdivisions; Epsilonproteobacteria; Campylobacterales; Helicobacteraceae Thiomicrospira denitrificans_ATCC_33889 Proteobacteria; delta/epsilon subdivisions; Epsilonproteobacteria; Campylobacterales; Helicobacteraceae * Wolinella succinogenes Proteobacteria; delta/epsilon subdivisions; Epsilonproteobacteria; Campylobacterales; Helicobacteraceae * Acinetobacter sp_ADP1 Proteobacteria; Gammaproteobacteria; Pseudomonadales; Moraxellaceae * Baumannia cicadellinicola_Homalodisca_c Proteobacteria; Gammaproteobacteria; unclassified Gammaproteobacteria Buchnera aphidicola str. APS (Acyrthosiphon pisum) Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae Buchnera aphidicola str. Bp (Baizongia pistaciae) Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae Buchnera aphidicola str. Sg (Schizaphis graminum) Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae Candidatus Blochmannia_floridanus Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; unclassified Enterobacteriaceae; ant, tsetse, mealybug, aphid, etc. endosymbionts; ant endosymbionts Candidatus Blochmannia_pennsylvanicus_B Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; unclassified Enterobacteriaceae; ant, tsetse, mealybug, aphid, etc. endosymbionts; ant endosymbionts Chromohalobacter salexigens_DSM_3043 Proteobacteria; Gammaproteobacteria; Oceanospirillales; Halomonadaceae * Colwellia psychrerythraea_34H Proteobacteria; Gammaproteobacteria; Alteromonadales; Colwelliaceae * Coxiella burnetii Proteobacteria; Gammaproteobacteria; ; Coxiellaceae Erwinia carotovora_atroseptica_SCRI1043 Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Escherichia coli_CFT073 Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Escherichia coli_K12 Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Escherichia coli_O157H7 Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae *

urbonavicus_MIE_2007_tableS1.xls 6 01/02/2007 Escherichia coli_O157H7_EDL933 Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Escherichia coli_UTI89 Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Francisella tularensis_holarctica Proteobacteria; Gammaproteobacteria; ; Francisellaceae Francisella tularensis_tularensis Proteobacteria; Gammaproteobacteria; Thiotrichales; Francisellaceae Haemophilus ducreyi_35000HP Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae * Haemophilus influenzae Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae * Haemophilus influenzae_86_028NP Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae * Hahella chejuensis_KCTC_2396 Proteobacteria; Gammaproteobacteria; Oceanospirillales; Hahellaceae; Hahella Idiomarina loihiensis_L2TR Proteobacteria; Gammaproteobacteria; Alteromonadales; Idiomarinaceae; Idiomarina * Legionella pneumophila_Lens Proteobacteria; Gammaproteobacteria; Legionellales; Legionellaceae Legionella pneumophila_Paris Proteobacteria; Gammaproteobacteria; Legionellales; Legionellaceae Legionella pneumophila_Philadelphia_1 Proteobacteria; Gammaproteobacteria; Legionellales; Legionellaceae Mannheimia succiniciproducens_MBEL55E Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae * Methylococcus capsulatus_Bath Proteobacteria; Gammaproteobacteria; Methylococcales; Nitrosococcus oceani_ATCC_19707 Proteobacteria; Gammaproteobacteria; Chromatiales; Chromatiaceae Pasteurella multocida Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae * Photobacterium profundum_SS9 Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae * Photorhabdus luminescens Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Pseudoalteromonas atlantica_T6c Proteobacteria; Gammaproteobacteria; Alteromonadales; Pseudoalteromonadaceae; Pseudoalteromonas; Pseudoalteromonas atlantica * Pseudoalteromonas haloplanktis_TAC125 Proteobacteria; Gammaproteobacteria; Alteromonadales; Pseudoalteromonadaceae; Pseudoalteromonas; Pseudoalteromonas atlantica * Pseudomonas aeruginosa Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae * Pseudomonas entomophila_L48 Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae * Pseudomonas fluorescens_Pf_5 Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae * Pseudomonas fluorescens_PfO_1 Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae * Pseudomonas putida_KT2440 Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae * Pseudomonas syringae_phaseolicola_1448A Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae * Pseudomonas syringae_pv_B728a Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae * Pseudomonas syringae_tomato_DC3000 Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae * Psychrobacter arcticum_273_4 Proteobacteria; Gammaproteobacteria; Pseudomonadales; Moraxellaceae Psychrobacter cryohalolentis_K5 Proteobacteria; Gammaproteobacteria; Pseudomonadales; Moraxellaceae Saccharophagus degradans_2_40 Proteobacteria; Gammaproteobacteria; Alteromonadales; Alteromonadaceae; Saccharophagus * Salmonella enterica_Choleraesuis Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Salmonella enterica_Paratypi_ATCC_9150 Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Salmonella typhi Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Salmonella typhi_Ty2 Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Salmonella typhimurium_LT2 Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Shewanella denitrificans_OS217 Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae * Shewanella oneidensis Proteobacteria; Gammaproteobacteria; Alteromonadales; Shewanellaceae * Shigella boydii_Sb227 Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Shigella dysenteriae Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Shigella flexneri_2a Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Shigella flexneri_2a_2457T Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Shigella sonnei_Ss046 Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Sodalis glossinidius_morsitans Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriace * Thiomicrospira crunogena_XCL_2 Proteobacteria; Gammaproteobacteria; Thiotrichales; Piscirickettsiaceae * Vibrio cholerae Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae * Vibrio fischeri_ES114 Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae * Vibrio parahaemolyticus Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae * Vibrio vulnificus_CMCP6 Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae * Vibrio vulnificus_YJ016 Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae * Wigglesworthia brevipalpis Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae

urbonavicus_MIE_2007_tableS1.xls 7 01/02/2007 axonopodis pv citri Proteobacteria; Gammaproteobacteria; Xanthomonadales; ; Xanthomonas pv. campestris str. ATCC 33913 Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Xanthomonas Xanthomonas campestris_8004 Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Xanthomonas Xanthomonas campestris_vesicatoria_851 Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Xanthomonas Xanthomonas oryzae_KACC10331 Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Xanthomonas Xanthomonas oryzae_MAFF_311018 Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Xanthomonas Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae Xylella fastidiosa_Temecula1 Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae Yersinia pestis_Antiqua Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Yersinia pestis_biovar_Mediaevails Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Yersinia pestis_CO92 Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Yersinia pestis_KIM Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Yersinia pestis_Nepal516 Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Yersinia pseudotuberculosis_IP32953 Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae * Borrelia burgdorferi Spirochaetes; Spirochaetes (class); Spirochaetales; Spirochaetaceae Borrelia garinii_PBi Spirochaetes; Spirochaetes (class); Spirochaetales; Spirochaetaceae Leptospira interrogans_serovar_Copenhag Spirochaetes; Spirochaetes (class); Spirochaetales; Leptospiraceae Leptospira interrogans_serovar_Lai Spirochaetes; Spirochaetes (class); Spirochaetales; Leptospiraceae Treponema denticola_ATCC_35405 Spirochaetes; Spirochaetes (class); Spirochaetales; Spirochaetaceae Treponema pallidum Spirochaetes; Spirochaetes (class); Spirochaetales; Spirochaetaceae Thermotoga maritima Thermotogae; Thermotogae (class); Thermotogales; Thermotogaceae *

urbonavicus_MIE_2007_tableS1.xls 8 01/02/2007