Table S1 All fully sequenced genome (09/30/08)

Taxon=archaea

Genome

Aeropyrum pernix K1 Archaeoglobus fulgidus DSM 4304 Caldivirga maquilingensis IC-167 Candidatus Korarchaeum cryptofilum OPF8 Candidatus Methanoregula boonei 6A8 Haloarcula marismortui ATCC 43049 Halobacterium salinarum R1 Halobacterium sp. NRC-1 Haloquadratum walsbyi DSM 16790 Hyperthermus butylicus DSM 5456 Ignicoccus hospitalis KIN4/I Metallosphaera sedula DSM 5348 Methanobrevibacter smithii ATCC 35061 Methanocaldococcus jannaschii DSM 2661 Methanococcoides burtonii DSM 6242 Methanococcus aeolicus Nankai-3 Methanococcus maripaludis C5 Methanococcus maripaludis C6 Methanococcus maripaludis C7 Methanococcus maripaludis S2 Methanococcus vannielii SB Methanocorpusculum labreanum Z Methanoculleus marisnigri JR1 Methanopyrus kandleri AV19 Methanosaeta thermophila PT Methanosarcina acetivorans C2A Methanosarcina barkeri str. Fusaro Methanosarcina mazei Go1 Methanosphaera stadtmanae DSM 3091 Methanospirillum hungatei JF-1 Methanothermobacter thermautotrophicus str. Delta H Nanoarchaeum equitans Kin4-M Natronomonas pharaonis DSM 2160 Nitrosopumilus maritimus SCM1 Picrophilus torridus DSM 9790 Pyrobaculum aerophilum str. IM2 Pyrobaculum arsenaticum DSM 13514 Pyrobaculum calidifontis JCM 11548 Pyrobaculum islandicum DSM 4184 Pyrococcus abyssi GE5 Pyrococcus furiosus DSM 3638 Pyrococcus horikoshii OT3 Staphylothermus marinus F1 Sulfolobus acidocaldarius DSM 639 Sulfolobus solfataricus P2 Sulfolobus tokodaii str. 7 Thermococcus kodakarensis KOD1 Thermofilum pendens Hrk 5 Thermoplasma acidophilum DSM 1728 Thermoplasma volcanium GSS1 Thermoproteus neutrophilus V24Sta uncultured methanogenic archaeon RC-I Taxon=bacteria Organism Acaryochloris marina MBIC11017 Acholeplasma laidlawii PG-8A Acidiphilium cryptum JF-5 Acidithiobacillus ferrooxidans ATCC 53993 Acidobacteria bacterium Ellin345 Acidothermus cellulolyticus 11B Acidovorax avenae subsp. citrulli AAC00-1 Acidovorax sp. JS42 Acinetobacter baumannii ACICU Acinetobacter baumannii ATCC 17978 Acinetobacter baumannii AYE Acinetobacter baumannii SDF Acinetobacter sp. ADP1 Actinobacillus pleuropneumoniae L20 Actinobacillus pleuropneumoniae serovar 3 str. JL03 Actinobacillus pleuropneumoniae serovar 7 str. AP76 Actinobacillus succinogenes 130Z Aeromonas hydrophila subsp. hydrophila ATCC 7966 Aeromonas salmonicida subsp. salmonicida A449 Agrobacterium tumefaciens str. C58 Akkermansia muciniphila ATCC BAA-835 Alcanivorax borkumensis SK2 Alkalilimnicola ehrlichei MLHE-1 Alkaliphilus metalliredigens QYMF Alkaliphilus oremlandii OhILAs Alteromonas macleodii 'Deep ecotype' Anabaena variabilis ATCC 29413 Anaeromyxobacter dehalogenans 2CP-C Anaeromyxobacter sp. Fw109-5 Anaeromyxobacter sp. K Anaplasma marginale str. St. Maries Anaplasma phagocytophilum HZ Aquifex aeolicus VF5 Arcobacter butzleri RM4018 Aromatoleum aromaticum EbN1 Arthrobacter aurescens TC1 Arthrobacter sp. FB24 Aster yellows witches'-broom phytoplasma AYWB Azoarcus sp. BH72 Azorhizobium caulinodans ORS 571 Bacillus amyloliquefaciens FZB42 Bacillus anthracis str. 'Ames Ancestor' Bacillus anthracis str. Ames Bacillus anthracis str. Sterne Bacillus cereus ATCC 10987 Bacillus cereus ATCC 14579 Bacillus cereus E33L Bacillus cereus subsp. cytotoxis NVH 391-98 Bacillus clausii KSM-K16 Bacillus halodurans C-125 Bacillus licheniformis ATCC 14580 Bacillus licheniformis ATCC 14580 Bacillus pumilus SAFR-032 Bacillus subtilis subsp. subtilis str. 168 Bacillus thuringiensis serovar konkukian str. 97-27 Bacillus thuringiensis str. Al Hakam Bacillus weihenstephanensis KBAB4 Bacteroides fragilis NCTC 9343 Bacteroides fragilis YCH46 Bacteroides thetaiotaomicron VPI-5482 Bacteroides vulgatus ATCC 8482 Bartonella bacilliformis KC583 Bartonella henselae str. Houston-1 Bartonella quintana str. Toulouse Bartonella tribocorum CIP 105476 Baumannia cicadellinicola str. Hc (Homalodisca coagulata) Bdellovibrio bacteriovorus HD100 Beijerinckia indica subsp. indica ATCC 9039 Bifidobacterium adolescentis ATCC 15703 Bifidobacterium longum DJO10A Bifidobacterium longum NCC2705 Bordetella avium 197N Bordetella bronchiseptica RB50 Bordetella parapertussis 12822 Bordetella pertussis Tohama I Bordetella petrii DSM 12804 Borrelia afzelii PKo Borrelia burgdorferi B31 Borrelia duttonii Ly Borrelia garinii PBi Borrelia hermsii DAH Borrelia recurrentis A1 Borrelia turicatae 91E135 Bradyrhizobium japonicum USDA 110 Bradyrhizobium sp. BTAi1 Bradyrhizobium sp. ORS278 Brucella abortus S19 Brucella abortus bv. 1 str. 9-941 Brucella canis ATCC 23365 Brucella melitensis 16M Brucella melitensis biovar Abortus 2308 Brucella ovis ATCC 25840 Brucella suis 1330 Brucella suis ATCC 23445 Buchnera aphidicola str. APS (Acyrthosiphon pisum) Buchnera aphidicola str. Bp (Baizongia pistaciae) Buchnera aphidicola str. Cc (Cinara cedri) Buchnera aphidicola str. Sg (Schizaphis graminum) Burkholderia ambifaria AMMD Burkholderia ambifaria MC40-6 Burkholderia cenocepacia AU 1054 Burkholderia cenocepacia HI2424 Burkholderia cenocepacia J2315 Burkholderia cenocepacia MC0-3 Burkholderia mallei ATCC 23344 Burkholderia mallei NCTC 10229 Burkholderia mallei NCTC 10247 Burkholderia mallei SAVP1 Burkholderia multivorans ATCC 17616 Burkholderia multivorans ATCC 17616 Burkholderia phymatum STM815 Burkholderia phytofirmans PsJN Burkholderia pseudomallei 1106a Burkholderia pseudomallei 1710b Burkholderia pseudomallei 668 Burkholderia pseudomallei K96243 Burkholderia sp. 383 Burkholderia thailandensis E264 Burkholderia vietnamiensis G4 Burkholderia xenovorans LB400 Caldicellulosiruptor saccharolyticus DSM 8903 Campylobacter concisus 13826 Campylobacter curvus 525.92 Campylobacter fetus subsp. fetus 82-40 Campylobacter hominis ATCC BAA-381 Campylobacter jejuni RM1221 Campylobacter jejuni subsp. doylei 269.97 Campylobacter jejuni subsp. jejuni 81-176 Campylobacter jejuni subsp. jejuni 81116 Campylobacter jejuni subsp. jejuni NCTC 11168 Candidatus Amoebophilus asiaticus 5a2 Candidatus Blochmannia floridanus Candidatus Blochmannia pennsylvanicus str. BPEN Candidatus Carsonella ruddii PV Candidatus Desulforudis audaxviator MP104C Candidatus Pelagibacter ubique HTCC1062 Candidatus Phytoplasma australiense Candidatus Phytoplasma mali Candidatus Protochlamydia amoebophila UWE25 Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica) Candidatus Sulcia muelleri GWSS Candidatus Vesicomyosocius okutanii HA Carboxydothermus hydrogenoformans Z-2901 Caulobacter crescentus CB15 Caulobacter sp. K31 Cellvibrio japonicus Ueda107 Chlamydia muridarum Nigg Chlamydia trachomatis 434/Bu Chlamydia trachomatis A/HAR-13 Chlamydia trachomatis D/UW-3/CX Chlamydia trachomatis L2b/UCH-1/proctitis Chlamydophila abortus S26/3 Chlamydophila caviae GPIC Chlamydophila felis Fe/C-56 Chlamydophila pneumoniae AR39 Chlamydophila pneumoniae CWL029 Chlamydophila pneumoniae J138 Chlamydophila pneumoniae TW-183 Chlorobaculum parvum NCIB 8327 Chlorobium chlorochromatii CaD3 Chlorobium limicola DSM 245 Chlorobium phaeobacteroides BS1 Chlorobium phaeobacteroides DSM 266 Chlorobium phaeovibrioides DSM 265 Chlorobium tepidum TLS Chloroflexus aurantiacus J-10-fl Chloroherpeton thalassium ATCC 35110 Chromobacterium violaceum ATCC 12472 Chromohalobacter salexigens DSM 3043 Citrobacter koseri ATCC BAA-895 Clavibacter michiganensis subsp. michiganensis NCPPB 382 Clavibacter michiganensis subsp. sepedonicus Clostridium acetobutylicum ATCC 824 Clostridium beijerinckii NCIMB 8052 Clostridium botulinum A str. ATCC 19397 Clostridium botulinum A str. ATCC 3502 Clostridium botulinum A str. Hall Clostridium botulinum A3 str. Loch Maree Clostridium botulinum B str. Eklund 17B Clostridium botulinum B1 str. Okra Clostridium botulinum E3 str. Alaska E43 Clostridium botulinum F str. Langeland Clostridium difficile 630 Clostridium kluyveri DSM 555 Clostridium novyi NT Clostridium perfringens ATCC 13124 Clostridium perfringens SM101 Clostridium perfringens str. 13 Clostridium phytofermentans ISDg Clostridium tetani E88 Clostridium thermocellum ATCC 27405 Colwellia psychrerythraea 34H Coprothermobacter proteolyticus DSM 5265 Corynebacterium diphtheriae NCTC 13129 Corynebacterium efficiens YS-314 Corynebacterium glutamicum ATCC 13032 Corynebacterium glutamicum ATCC 13032 Corynebacterium glutamicum R Corynebacterium jeikeium K411 Corynebacterium urealyticum DSM 7109 Coxiella burnetii Dugway 5J108-111 Coxiella burnetii RSA 331 Coxiella burnetii RSA 493 Cupriavidus taiwanensis Cyanothece sp. ATCC 51142 Cytophaga hutchinsonii ATCC 33406 Dechloromonas aromatica RCB Dehalococcoides ethenogenes 195 Dehalococcoides sp. BAV1 Dehalococcoides sp. CBDB1 Deinococcus geothermalis DSM 11300 Deinococcus radiodurans R1 Delftia acidovorans SPH-1 Desulfitobacterium hafniense Y51 Desulfococcus oleovorans Hxd3 Desulfotalea psychrophila LSv54 Desulfotomaculum reducens MI-1 Desulfovibrio desulfuricans subsp. desulfuricans str. G20 Desulfovibrio vulgaris subsp. vulgaris DP4 Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough Dichelobacter nodosus VCS1703A Dictyoglomus thermophilum H-6-12 Dinoroseobacter shibae DFL 12 Ehrlichia canis str. Jake Ehrlichia chaffeensis str. Arkansas Ehrlichia ruminantium str. Gardel Ehrlichia ruminantium str. Welgevonden Ehrlichia ruminantium str. Welgevonden Elusimicrobium minutum Pei191 Enterobacter sakazakii ATCC BAA-894 Enterobacter sp. 638 Enterococcus faecalis V583 Erwinia tasmaniensis Erythrobacter litoralis HTCC2594 Escherichia coli 536 Escherichia coli APEC O1 Escherichia coli ATCC 8739 Escherichia coli CFT073 Escherichia coli E24377A Escherichia coli HS Escherichia coli O157:H7 EDL933 Escherichia coli O157:H7 str. Sakai Escherichia coli SMS-3-5 Escherichia coli UTI89 Escherichia coli str. K12 substr. DH10B Escherichia coli str. K12 substr. MG1655 Escherichia coli str. K12 substr. W3110 Exiguobacterium sibiricum 255-15 Fervidobacterium nodosum Rt17-B1 Finegoldia magna ATCC 29328 Flavobacterium johnsoniae UW101 Flavobacterium psychrophilum JIP02/86 Francisella novicida U112 Francisella philomiragia subsp. philomiragia ATCC 25017 Francisella tularensis subsp. holarctica Francisella tularensis subsp. holarctica FTNF002-00 Francisella tularensis subsp. holarctica OSU18 Francisella tularensis subsp. mediasiatica FSC147 Francisella tularensis subsp. tularensis FSC198 Francisella tularensis subsp. tularensis SCHU S4 Francisella tularensis subsp. tularensis WY96-3418 Frankia alni ACN14a Frankia sp. CcI3 Frankia sp. EAN1pec Fusobacterium nucleatum subsp. nucleatum ATCC 25586 Geobacillus kaustophilus HTA426 Geobacillus thermodenitrificans NG80-2 Geobacter bemidjiensis Bem Geobacter lovleyi SZ Geobacter metallireducens GS-15 Geobacter sulfurreducens PCA Geobacter uraniireducens Rf4 Gloeobacter violaceus PCC 7421 Gluconacetobacter diazotrophicus PAl 5 Gluconobacter oxydans 621H Gramella forsetii KT0803 Granulibacter bethesdensis CGDNIH1 Haemophilus ducreyi 35000HP Haemophilus influenzae 86-028NP Haemophilus influenzae PittEE Haemophilus influenzae PittGG Haemophilus influenzae Rd KW20 Haemophilus somnus 129PT Haemophilus somnus 2336 Hahella chejuensis KCTC 2396 Halorhodospira halophila SL1 Helicobacter acinonychis str. Sheeba Helicobacter hepaticus ATCC 51449 Helicobacter pylori 26695 Helicobacter pylori HPAG1 Helicobacter pylori J99 Helicobacter pylori Shi470 Heliobacterium modesticaldum Ice1 Herminiimonas arsenicoxydans Herpetosiphon aurantiacus ATCC 23779 Hydrogenobaculum sp. Y04AAS1 Hyphomonas neptunium ATCC 15444 Idiomarina loihiensis L2TR Jannaschia sp. CCS1 Janthinobacterium sp. Marseille Kineococcus radiotolerans SRS30216 Klebsiella pneumoniae 342 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 Kocuria rhizophila DC2201 Lactobacillus acidophilus NCFM Lactobacillus brevis ATCC 367 Lactobacillus casei ATCC 334 Lactobacillus casei BL23 Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 Lactobacillus fermentum IFO 3956 Lactobacillus gasseri ATCC 33323 Lactobacillus helveticus DPC 4571 Lactobacillus johnsonii NCC 533 Lactobacillus plantarum WCFS1 Lactobacillus reuteri F275 Lactobacillus reuteri F275 Lactobacillus sakei subsp. sakei 23K Lactobacillus salivarius UCC118 Lactococcus lactis subsp. cremoris MG1363 Lactococcus lactis subsp. cremoris SK11 Lactococcus lactis subsp. lactis Il1403 Lawsonia intracellularis PHE/MN1-00 Legionella pneumophila str. Corby Legionella pneumophila str. Lens Legionella pneumophila str. Paris Legionella pneumophila subsp. pneumophila str. Philadelphia 1 Leifsonia xyli subsp. xyli str. CTCB07 Leptospira biflexa serovar Patoc strain 'Patoc 1 (Ames)' Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)' Leptospira borgpetersenii serovar Hardjo-bovis JB197 Leptospira borgpetersenii serovar Hardjo-bovis L550 Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 Leptospira interrogans serovar Lai str. 56601 Leptothrix cholodnii SP-6 Leuconostoc citreum KM20 Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 Listeria innocua Clip11262 Listeria monocytogenes EGD-e Listeria monocytogenes str. 4b F2365 Listeria welshimeri serovar 6b str. SLCC5334 Lysinibacillus sphaericus C3-41 Magnetococcus sp. MC-1 Magnetospirillum magneticum AMB-1 Mannheimia succiniciproducens MBEL55E Maricaulis maris MCS10 Marinobacter aquaeolei VT8 Marinomonas sp. MWYL1 Mesoplasma florum L1 Mesorhizobium loti MAFF303099 Mesorhizobium sp. BNC1 Methylacidiphilum infernorum V4 Methylibium petroleiphilum PM1 Methylobacillus flagellatus KT Methylobacterium extorquens PA1 Methylobacterium populi BJ001 Methylobacterium radiotolerans JCM 2831 Methylobacterium sp. 4-46 Methylococcus capsulatus str. Bath Microcystis aeruginosa NIES-843 Moorella thermoacetica ATCC 39073 Mycobacterium abscessus Mycobacterium avium 104 Mycobacterium avium subsp. paratuberculosis K-10 Mycobacterium bovis AF2122/97 Mycobacterium bovis BCG str. Pasteur 1173P2 Mycobacterium gilvum PYR-GCK Mycobacterium leprae TN Mycobacterium marinum M Mycobacterium smegmatis str. MC2 155 Mycobacterium sp. JLS Mycobacterium sp. KMS Mycobacterium sp. MCS Mycobacterium tuberculosis CDC1551 Mycobacterium tuberculosis F11 Mycobacterium tuberculosis H37Ra Mycobacterium tuberculosis H37Rv Mycobacterium ulcerans Agy99 Mycobacterium vanbaalenii PYR-1 Mycoplasma agalactiae PG2 Mycoplasma arthritidis 158L3-1 Mycoplasma capricolum subsp. capricolum ATCC 27343 Mycoplasma gallisepticum R Mycoplasma genitalium G37 Mycoplasma hyopneumoniae 232 Mycoplasma hyopneumoniae 7448 Mycoplasma hyopneumoniae J Mycoplasma mobile 163K Mycoplasma mycoides subsp. mycoides SC str. PG1 Mycoplasma penetrans HF-2 Mycoplasma pneumoniae M129 Mycoplasma pulmonis UAB CTIP Mycoplasma synoviae 53 Myxococcus xanthus DK 1622 Natranaerobius thermophilus JW/NM-WN-LF Neisseria gonorrhoeae FA 1090 Neisseria gonorrhoeae NCCP11945 Neisseria meningitidis 053442 Neisseria meningitidis FAM18 Neisseria meningitidis MC58 Neisseria meningitidis Z2491 Neorickettsia sennetsu str. Miyayama Nitratiruptor sp. SB155-2 Nitrobacter hamburgensis X14 Nitrobacter winogradskyi Nb-255 Nitrosococcus oceani ATCC 19707 Nitrosomonas europaea ATCC 19718 Nitrosomonas eutropha C91 Nitrosospira multiformis ATCC 25196 Nocardia farcinica IFM 10152 Nocardioides sp. JS614 Nostoc punctiforme PCC 73102 Nostoc sp. PCC 7120 Novosphingobium aromaticivorans DSM 12444 Oceanobacillus iheyensis HTE831 Ochrobactrum anthropi ATCC 49188 Oenococcus oeni PSU-1 Onion yellows phytoplasma OY-M Opitutus terrae PB90-1 Orientia tsutsugamushi str. Boryong Orientia tsutsugamushi str. Ikeda Parabacteroides distasonis ATCC 8503 Paracoccus denitrificans PD1222 Parvibaculum lavamentivorans DS-1 Pasteurella multocida subsp. multocida str. Pm70 Pectobacterium atrosepticum SCRI1043 Pediococcus pentosaceus ATCC 25745 Pelobacter carbinolicus DSM 2380 Pelobacter propionicus DSM 2379 Pelodictyon luteolum DSM 273 Pelodictyon phaeoclathratiforme BU-1 Pelotomaculum thermopropionicum SI Petrotoga mobilis SJ95 Phenylobacterium zucineum HLK1 Photobacterium profundum SS9 Photorhabdus luminescens subsp. laumondii TTO1 Polaromonas naphthalenivorans CJ2 Polaromonas sp. JS666 Polynucleobacter necessarius STIR1 Polynucleobacter sp. QLW-P1DMWA-1 Porphyromonas gingivalis ATCC 33277 Porphyromonas gingivalis W83 Prochlorococcus marinus str. AS9601 Prochlorococcus marinus str. MIT 9211 Prochlorococcus marinus str. MIT 9215 Prochlorococcus marinus str. MIT 9301 Prochlorococcus marinus str. MIT 9303 Prochlorococcus marinus str. MIT 9312 Prochlorococcus marinus str. MIT 9313 Prochlorococcus marinus str. MIT 9515 Prochlorococcus marinus str. NATL1A Prochlorococcus marinus str. NATL2A Prochlorococcus marinus subsp. marinus str. CCMP1375 Prochlorococcus marinus subsp. pastoris str. CCMP1986 Propionibacterium acnes KPA171202 Prosthecochloris aestuarii DSM 271 Proteus mirabilis HI4320 Pseudoalteromonas atlantica T6c Pseudoalteromonas haloplanktis TAC125 Pseudomonas aeruginosa PA7 Pseudomonas aeruginosa PAO1 Pseudomonas aeruginosa UCBPP-PA14 Pseudomonas entomophila L48 Pseudomonas fluorescens Pf-5 Pseudomonas fluorescens Pf0-1 Pseudomonas mendocina ymp Pseudomonas putida F1 Pseudomonas putida GB-1 Pseudomonas putida KT2440 Pseudomonas putida W619 Pseudomonas stutzeri A1501 Pseudomonas syringae pv. phaseolicola 1448A Pseudomonas syringae pv. syringae B728a Pseudomonas syringae pv. tomato str. DC3000 Psychrobacter arcticus 273-4 Psychrobacter cryohalolentis K5 Psychrobacter sp. PRwf-1 Psychromonas ingrahamii 37 Ralstonia eutropha H16 Ralstonia eutropha JMP134 Ralstonia metallidurans CH34 Ralstonia pickettii 12J Ralstonia solanacearum GMI1000 Renibacterium salmoninarum ATCC 33209 Rhizobium etli CFN 42 Rhizobium etli CIAT 652 Rhizobium leguminosarum bv. viciae 3841 Rhodobacter sphaeroides 2.4.1 Rhodobacter sphaeroides ATCC 17025 Rhodobacter sphaeroides ATCC 17029 Rhodococcus sp. RHA1 Rhodoferax ferrireducens T118 Rhodopirellula baltica SH 1 Rhodopseudomonas palustris BisA53 Rhodopseudomonas palustris BisB18 Rhodopseudomonas palustris BisB5 Rhodopseudomonas palustris CGA009 Rhodopseudomonas palustris HaA2 Rhodopseudomonas palustris TIE-1 Rhodospirillum rubrum ATCC 11170 Rickettsia akari str. Hartford Rickettsia bellii OSU 85-389 Rickettsia bellii RML369-C Rickettsia canadensis str. McKiel Rickettsia conorii str. Malish 7 Rickettsia felis URRWXCal2 Rickettsia massiliae MTU5 Rickettsia prowazekii str. Madrid E Rickettsia rickettsii str. 'Sheila Smith' Rickettsia rickettsii str. Iowa Rickettsia typhi str. Wilmington Roseiflexus castenholzii DSM 13941 Roseiflexus sp. RS-1 Roseobacter denitrificans OCh 114 Rubrobacter xylanophilus DSM 9941 Saccharophagus degradans 2-40 Saccharopolyspora erythraea NRRL 2338 Salinibacter ruber DSM 13855 Salinispora arenicola CNS-205 Salinispora tropica CNB-440 Salmonella enterica subsp. arizonae serovar 62:z4,z23:-- Salmonella enterica subsp. enterica serovar Agona str. SL483 Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853 Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91 Salmonella enterica subsp. enterica serovar Heidelberg str. SL476 Salmonella enterica subsp. enterica serovar Newport str. SL254 Salmonella enterica subsp. enterica serovar Paratyphi A str. AKU_12601 Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7 Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633 Salmonella enterica subsp. enterica serovar Typhi str. CT18 Salmonella enterica subsp. enterica serovar Typhi str. Ty2 Salmonella typhimurium LT2 Serratia proteamaculans 568 Shewanella amazonensis SB2B Shewanella baltica OS155 Shewanella baltica OS185 Shewanella baltica OS195 Shewanella denitrificans OS217 Shewanella frigidimarina NCIMB 400 Shewanella halifaxensis HAW-EB4 Shewanella loihica PV-4 Shewanella oneidensis MR-1 Shewanella pealeana ATCC 700345 Shewanella putrefaciens CN-32 Shewanella sediminis HAW-EB3 Shewanella sp. ANA-3 Shewanella sp. MR-4 Shewanella sp. MR-7 Shewanella sp. W3-18-1 Shewanella woodyi ATCC 51908 Shigella boydii CDC 3083-94 Shigella boydii Sb227 Shigella dysenteriae Sd197 Shigella flexneri 2a str. 2457T Shigella flexneri 2a str. 301 Shigella flexneri 5 str. 8401 Shigella sonnei Ss046 Silicibacter pomeroyi DSS-3 Silicibacter sp. TM1040 Sinorhizobium medicae WSM419 Sinorhizobium meliloti 1021 Sodalis glossinidius str. 'morsitans' Solibacter usitatus Ellin6076 Sorangium cellulosum 'So ce 56' Sphingomonas wittichii RW1 Sphingopyxis alaskensis RB2256 Staphylococcus aureus RF122 Staphylococcus aureus subsp. aureus COL Staphylococcus aureus subsp. aureus JH1 Staphylococcus aureus subsp. aureus JH9 Staphylococcus aureus subsp. aureus MRSA252 Staphylococcus aureus subsp. aureus MSSA476 Staphylococcus aureus subsp. aureus MW2 Staphylococcus aureus subsp. aureus Mu3 Staphylococcus aureus subsp. aureus Mu50 Staphylococcus aureus subsp. aureus N315 Staphylococcus aureus subsp. aureus NCTC 8325 Staphylococcus aureus subsp. aureus USA300 Staphylococcus aureus subsp. aureus USA300_TCH1516 Staphylococcus aureus subsp. aureus str. Newman Staphylococcus epidermidis ATCC 12228 Staphylococcus epidermidis RP62A Staphylococcus haemolyticus JCSC1435 Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 Stenotrophomonas maltophilia K279a Stenotrophomonas maltophilia R551-3 Streptococcus agalactiae 2603V/R Streptococcus agalactiae A909 Streptococcus agalactiae NEM316 Streptococcus equi subsp. zooepidemicus MGCS10565 Streptococcus gordonii str. Challis substr. CH1 Streptococcus mutans UA159 Streptococcus pneumoniae CGSP14 Streptococcus pneumoniae D39 Streptococcus pneumoniae G54 Streptococcus pneumoniae Hungary19A-6 Streptococcus pneumoniae R6 Streptococcus pneumoniae TIGR4 Streptococcus pyogenes M1 GAS Streptococcus pyogenes MGAS10270 Streptococcus pyogenes MGAS10394 Streptococcus pyogenes MGAS10750 Streptococcus pyogenes MGAS2096 Streptococcus pyogenes MGAS315 Streptococcus pyogenes MGAS5005 Streptococcus pyogenes MGAS6180 Streptococcus pyogenes MGAS8232 Streptococcus pyogenes MGAS9429 Streptococcus pyogenes SSI-1 Streptococcus pyogenes str. Manfredo Streptococcus sanguinis SK36 Streptococcus suis 05ZYH33 Streptococcus suis 98HAH33 Streptococcus thermophilus CNRZ1066 Streptococcus thermophilus LMD-9 Streptococcus thermophilus LMG 18311 Streptomyces avermitilis MA-4680 Streptomyces coelicolor A3(2) Streptomyces griseus subsp. griseus NBRC 13350 Sulfurihydrogenibium sp. YO3AOP1 Sulfurimonas denitrificans DSM 1251 Sulfurovum sp. NBC37-1 Symbiobacterium thermophilum IAM 14863 Synechococcus elongatus PCC 6301 Synechococcus elongatus PCC 7942 Synechococcus sp. CC9311 Synechococcus sp. CC9605 Synechococcus sp. CC9902 Synechococcus sp. JA-2-3B'a(2-13) Synechococcus sp. JA-3-3Ab Synechococcus sp. PCC 7002 Synechococcus sp. RCC307 Synechococcus sp. WH 7803 Synechococcus sp. WH 8102 Synechocystis sp. PCC 6803 Syntrophobacter fumaroxidans MPOB Syntrophomonas wolfei subsp. wolfei str. Goettingen Syntrophus aciditrophicus SB Thermoanaerobacter pseudethanolicus ATCC 33223 Thermoanaerobacter sp. X514 Thermoanaerobacter tengcongensis MB4 Thermobifida fusca YX Thermodesulfovibrio yellowstonii DSM 11347 Thermosipho melanesiensis BI429 Thermosynechococcus elongatus BP-1 Thermotoga lettingae TMO Thermotoga maritima MSB8 Thermotoga petrophila RKU-1 Thermotoga sp. RQ2 Thermus thermophilus HB27 Thermus thermophilus HB8 Thiobacillus denitrificans ATCC 25259 Thiomicrospira crunogena XCL-2 Treponema denticola ATCC 35405 Treponema pallidum subsp. pallidum SS14 Treponema pallidum subsp. pallidum str. Nichols Trichodesmium erythraeum IMS101 Tropheryma whipplei TW08/27 Tropheryma whipplei str. Twist Ureaplasma parvum serovar 3 str. ATCC 27815 Ureaplasma parvum serovar 3 str. ATCC 700970 Verminephrobacter eiseniae EF01-2 Vibrio cholerae O1 biovar El Tor str. N16961 Vibrio cholerae O395 Vibrio fischeri ES114 Vibrio fischeri MJ11 Vibrio harveyi ATCC BAA-1116 Vibrio parahaemolyticus RIMD 2210633 Vibrio vulnificus CMCP6 Vibrio vulnificus YJ016 Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis Wolbachia endosymbiont of Drosophila melanogaster Wolbachia endosymbiont strain TRS of Brugia malayi Wolbachia pipientis Wolinella succinogenes DSM 1740 Xanthobacter autotrophicus Py2 Xanthomonas axonopodis pv. citri str. 306 Xanthomonas campestris pv. campestris str. B100 Xanthomonas campestris pv. campestris str. 8004 Xanthomonas campestris pv. campestris str. ATCC 33913 Xanthomonas campestris pv. vesicatoria str. 85-10 Xanthomonas oryzae pv. oryzae KACC10331 Xanthomonas oryzae pv. oryzae MAFF 311018 Xanthomonas oryzae pv. oryzae PXO99A Xylella fastidiosa 9a5c Xylella fastidiosa M12 Xylella fastidiosa M23 Xylella fastidiosa Temecula1 Yersinia enterocolitica subsp. enterocolitica 8081 Yersinia pestis Angola Yersinia pestis Antiqua Yersinia pestis CO92 Yersinia pestis KIM Yersinia pestis Nepal516 Yersinia pestis Pestoides F Yersinia pestis biovar Microtus str. 91001 Yersinia pseudotuberculosis IP 31758 Yersinia pseudotuberculosis IP 32953 Yersinia pseudotuberculosis PB1/+ Yersinia pseudotuberculosis YPIII Zymomonas mobilis subsp. mobilis ZM4

Table 2. Accession numbers for genomes used for 5S rRNA identification

Taxon = archaea

NC_009637,NC_001732,NC_009515,NC_000854,NC_010085,NC_002607,NC_009073,NC_007426,NC_000961 ,NC_008942,NC_009135,NC_009776,NC_008553,NC_010525,NC_008701,NC_009712,NC_009051,NC_00869 8,NC_007181,NC_009440,NC_008212,NC_000917,NC_008818,NC_001733,NC_009464,NC_005877,NC_0093 76,NC_010364,NC_007681,NC_003364,NC_006397,NC_002754,NC_009975,NC_007955,NC_010482,NC_009 635,NC_009033,NC_009954,NC_007355

Taxon = bacteria

NC_007429,NC_007974,NC_010718,NC_000919,NC_010516,NC_011297,NC_006142,NC_009648,NC_007650 ,NC_007482,NC_007516,NC_008261,NC_008525,NC_010524,NC_000921,NC_009428,NC_004461,NC_00945 5,NC_008347,NC_009012,NC_008700,NC_008044,NC_006841,NC_010475,NC_007204,NC_005810,NC_0105 05,NC_000117,NC_005070,NC_009840,NC_009483,NC_010634,NC_011126,NC_004113,NC_009719,NC_0077 98,NC_009663,NC_005042,NC_007776,NC_009614,NC_010170,NC_009253,NC_003103,NC_008816,NC_008 536,NC_007795,NC_003869,NC_009714,NC_009613,NC_009664,NC_004757,NC_008095,NC_009254,NC_00 5955,NC_010530,NC_010547,NC_006360,NC_010397,NC_007925,NC_007952,NC_010644,NC_002945,NC_0 11026,NC_007958,NC_007575,NC_006156,NC_007633,NC_007644,NC_006831,NC_008509,NC_009656,NC_ 010698,NC_010676,NC_008699,NC_005303,NC_009802,NC_007984,NC_009972,NC_010336,NC_008340,NC _002977,NC_008555,NC_010803,NC_009699,NC_001264,NC_008086,NC_009337,NC_002696,NC_008528,N C_010424,NC_009953,NC_008751,NC_008726,NC_011138,NC_002506,NC_011145,NC_009497,NC_006138,N C_009632,NC_010511,NC_010831,NC_008510,NC_007384,NC_008027,NC_010681,NC_009441,NC_009436, NC_009882,NC_008229,NC_002179,NC_007973,NC_008254,NC_011094,NC_010515,NC_009641,NC_010125 ,NC_009091,NC_005363,NC_010321,NC_009445,NC_008789,NC_008710,NC_010999,NC_002771,NC_00306 3,NC_000922,NC_008011,NC_009697,NC_008526,NC_007356,NC_009850,NC_008262,NC_010263,NC_0091 40,NC_010729,NC_010723,NC_002952,NC_007481,NC_010287,NC_008268,NC_008312,NC_006055,NC_007 294,NC_010571,NC_008570,NC_010678,NC_011184,NC_008344,NC_009456,NC_009901,NC_009976,NC_01 0338,NC_007964,NC_008709,NC_010814,NC_007332,NC_010104,NC_009783,NC_009617,NC_007775,NC_0 10003,NC_009767,NC_004369,NC_007492,NC_004557,NC_010730,NC_007498,NC_009480,NC_009943,NC_ 007576,NC_011025,NC_009053,NC_010740,NC_002488,NC_009487,NC_007406,NC_009513,NC_007951,NC _010544,NC_009257,NC_007335,NC_005956,NC_010079,NC_009667,NC_009784,NC_007778,NC_008435,N C_007348,NC_008609,NC_011060,NC_004842,NC_007969,NC_006351,NC_007880,NC_007963,NC_010602, NC_009085,NC_007109,NC_009655,NC_008820,NC_008599,NC_010471,NC_006832,NC_008593,NC_005090 ,NC_011146,NC_002505,NC_008752,NC_007512,NC_007948,NC_010280,NC_008061,NC_005125,NC_00967 4,NC_007761,NC_010520,NC_010994,NC_010611,NC_008610,NC_009078,NC_007907,NC_007520,NC_0094 42,NC_007899,NC_009881,NC_010682,NC_007759,NC_004605,NC_006576,NC_008463,NC_010581,NC_010 512,NC_010845,NC_010468,NC_008513,NC_010528,NC_007613,NC_009706,NC_010118,NC_009698,NC_00 8554,NC_007940,NC_011144,NC_003318,NC_008750,NC_009138,NC_009828,NC_007484,NC_009925,NC_0 09952,NC_000915,NC_008511,NC_010830,NC_009379,NC_009749,NC_009633,NC_008786,NC_008358,NC_ 008255,NC_009437,NC_007802,NC_009883,NC_008228,NC_011071,NC_006677,NC_008618,NC_004311,NC _010546,NC_010531,NC_007794,NC_009715,NC_007677,NC_005824,NC_011229,NC_008209,NC_007503,N C_011027,NC_002939,NC_010645,NC_009485,NC_007404,NC_009511,NC_007953,NC_009831,NC_008048, NC_010503,NC_010473,NC_008508,NC_002755,NC_004663,NC_007645,NC_002976,NC_010337,NC_009523 ,NC_009997,NC_008601,NC_010677,NC_010794,NC_009454,NC_009879,NC_008346,NC_009524,NC_00446 0,NC_010793,NC_005071,NC_008825,NC_002758,NC_008578,NC_008148,NC_009720,NC_010278,NC_0102 96,NC_007929,NC_009488,NC_008309,NC_007954,NC_009482,NC_009328,NC_007347,NC_008817,NC_009 718,NC_007799,NC_009615,NC_009662,NC_010001,NC_005823,NC_008781,NC_007908,NC_011001,NC_00 9077,NC_000912,NC_007626,NC_010410,NC_011296,NC_010483,NC_008260,NC_007947,NC_009142,NC_0 11134,NC_002950,NC_009922,NC_007517,NC_007614,NC_010162,NC_007354,NC_007513,NC_003366,NC_ 010628,NC_010725,NC_010655,NC_007519,NC_009495,NC_008369,NC_004432,NC_010556,NC_010995,NC _011244,NC_009348,NC_007350,NC_009778,NC_007760,NC_009675,NC_003902,NC_009443,NC_009434,N C_010610,NC_008611,NC_008785,NC_008512,NC_002745,NC_010519,NC_008025,NC_009486,NC_008277, NC_003272,NC_009052,NC_010741,NC_008740,NC_007494,NC_007577,NC_008819,NC_006085,NC_005140 ,NC_007797,NC_010175,NC_009785,NC_010545,NC_010674,NC_007005,NC_008245,NC_002162,NC_01033 4,NC_008705,NC_010609,NC_007298,NC_010407,NC_007292,NC_008576,NC_009654,NC_008146,NC_0096 59,NC_008595,NC_010400,NC_009380,NC_006933,NC_004350,NC_008571,NC_005072,NC_000908,NC_004 129,NC_010673,NC_007912,NC_008345,NC_009900,NC_008702,NC_009089,NC_007604,NC_008009,NC_00 9616,NC_010981,NC_003198,NC_007333,NC_009481,NC_005773,NC_002940,NC_002937,NC_009465,NC_0 07722,NC_005061,NC_011206,NC_004343,NC_010843,NC_010939,NC_011295,NC_006570,NC_005085,NC_ 000911,NC_008711,NC_010320,NC_009439,NC_008782,NC_010617,NC_002677,NC_009338,NC_010161,NC _000853,NC_003062,NC_009921,NC_007514,NC_011047,NC_010658,NC_007413,NC_008380,NC_008319 Table 3. Accession numbers for genomes used for 16S rRNA identification

Taxon = archaea

NC_001732,NC_003106,NC_000854,NC_010085,NC_007426,NC_009135,NC_009776,NC_008701,NC_002689 ,NC_003551,NC_003413,NC_001733,NC_005877,NC_005213,NC_010364,NC_010482,NC_009954

Taxon = bacteria

NC_008687,NC_006142,NC_007482,NC_009455,NC_006087,NC_010547,NC_006156,NC_008509,NC_001264 ,NC_008528,NC_008726,NC_002506,NC_009091,NC_008710,NC_007356,NC_009140,NC_009456,NC_00293 6,NC_009943,NC_011025,NC_004842,NC_002491,NC_008061,NC_010557,NC_008610,NC_005364,NC_0108 45,NC_010118,NC_010086,NC_007940,NC_008511,NC_010830,NC_008358,NC_005824,NC_011229,NC_0079 53,NC_008048,NC_008578,NC_008148,NC_006908,NC_000912,NC_007354,NC_010805,NC_010513,NC_008 512,NC_004344,NC_009565,NC_008277,NC_007577,NC_007797,NC_002162,NC_006833,NC_010673,NC_00 2978,NC_008009,NC_004556,NC_004343,NC_010843,NC_011295,NC_004545 Table 3. Accession numbers for genomes used for 23S rRNA identification

Taxon = archaea

NC_009637,NC_001732,NC_009515,NC_003106,NC_003552,NC_010085,NC_009073,NC_007426,NC_000961 ,NC_008942,NC_000868,NC_009135,NC_009776,NC_008553,NC_010525,NC_008701,NC_002689,NC_00971 2,NC_009051,NC_008698,NC_003901,NC_003551,NC_003413,NC_009440,NC_000917,NC_005791,NC_0088 18,NC_007796,NC_000909,NC_001733,NC_009464,NC_005877,NC_009376,NC_005213,NC_007681,NC_003 364,NC_002754,NC_009975,NC_007955,NC_010482,NC_009635,NC_009033,NC_009954,NC_007355

Taxon = bacteria

NC_007429,NC_000919,NC_007482,NC_007516,NC_004917,NC_010163,NC_009455,NC_008044,NC_006841 ,NC_010475,NC_010505,NC_007297,NC_005070,NC_009840,NC_011126,NC_004113,NC_002942,NC_002935 ,NC_009719,NC_007798,NC_009663,NC_005042,NC_007776,NC_008816,NC_008541,NC_003869,NC_00971 4,NC_006087,NC_004757,NC_005955,NC_010547,NC_010397,NC_009484,NC_010644,NC_009937,NC_0075 75,NC_007633,NC_006831,NC_008509,NC_008497,NC_004668,NC_008699,NC_005303,NC_010336,NC_001 264,NC_002696,NC_008528,NC_010424,NC_009953,NC_011035,NC_002506,NC_011145,NC_009497,NC_007 164,NC_002179,NC_008254,NC_010612,NC_010842,NC_009091,NC_010321,NC_008789,NC_008710,NC_00 2771,NC_010184,NC_000922,NC_010117,NC_008526,NC_004307,NC_007356,NC_010263,NC_009140,NC_0 08268,NC_008312,NC_006055,NC_007294,NC_010571,NC_010506,NC_010678,NC_008344,NC_009456,NC_ 009976,NC_010338,NC_010814,NC_010003,NC_009767,NC_004369,NC_002936,NC_007498,NC_009480,NC _011025,NC_007406,NC_010544,NC_005956,NC_009784,NC_008609,NC_004842,NC_007880,NC_010602,N C_008820,NC_006832,NC_002928,NC_007948,NC_005125,NC_003454,NC_003909,NC_007716,NC_008610, NC_005364,NC_009881,NC_002967,NC_004605,NC_010845,NC_008513,NC_010086,NC_007940,NC_011144 ,NC_009138,NC_009828,NC_009952,NC_008511,NC_010830,NC_009633,NC_008358,NC_007802,NC_00988 3,NC_008228,NC_008618,NC_010546,NC_007677,NC_005824,NC_011229,NC_008209,NC_004552,NC_0075 03,NC_002944,NC_006361,NC_007953,NC_010503,NC_008508,NC_004663,NC_009727,NC_010337,NC_009 523,NC_008601,NC_010677,NC_010794,NC_011186,NC_002971,NC_009454,NC_009879,NC_008346,NC_01 0793,NC_005071,NC_008825,NC_007296,NC_007205,NC_010296,NC_009488,NC_009482,NC_008817,NC_0 10816,NC_009718,NC_007799,NC_005043,NC_010001,NC_006908,NC_007168,NC_004829,NC_006347,NC_ 008686,NC_000912,NC_007947,NC_011134,NC_005027,NC_007354,NC_007513,NC_008369,NC_004432,NC _006371,NC_010995,NC_011244,NC_007350,NC_007760,NC_009675,NC_011072,NC_010610,NC_008611,NC _008025,NC_009486,NC_009512,NC_008277,NC_010741,NC_007577,NC_006085,NC_003911,NC_007797,N C_010175,NC_009785,NC_008533,NC_010545,NC_008245,NC_002162,NC_005295,NC_007298,NC_009659, NC_008595,NC_009380,NC_005072,NC_000908,NC_004129,NC_010673,NC_002978,NC_007912,NC_008009 ,NC_009616,NC_007333,NC_009481,NC_005773,NC_009465,NC_004343,NC_010843,NC_011295,NC_00871 1,NC_010320,NC_010617,NC_004545,NC_011047,NC_007413 Table S5. Prediction Performance for RNAmmer

Length of Reads Sensitivity Specificity 5S 16S 23S 5S 16S 23S 100 37.4 0 0 94.6 NA NA 200 61.3 0 0 94.5 NA NA 300 72.5 0 0 95.9 NA NA 400 76.7 0 0 95.6 NA NA 500 80.8 0 0 95.8 NA NA 600 82.1 0 0 95.5 NA NA 700 83.7 0 0 96.2 NA NA 800 87.3 2.5 0 94.7 1 NA

All sensitivities and specificities are represented in percentage (%).