Table S1. List of 168 genomes used in extended datasets detection.

Acinetobacter sp. ADP1
Aeropyrum pernix
Archaeoglobus fulgidus
Anaplasma marginale St Maries
Aquifex aeolicus
Agrobacterium tumifaciens C58 Cereon
Agrobacterium tumifaciens C58 U Wash
Azoarcus sp EbN1
Bacillus anthracis str. "Ames Ancestor"
Buchnera aphidicola
Bdellovibrio bacteriovorus HD100
Bordetella bronchiseptica RB50
Borrelia burgdorferi
Bacillus cereus ATCC 10987
Bacillus clausii KSM-K16
Blochmannia floridanus
Bacteroides fragilis YCH46
Borrelia garinii PBi
Bacillus halodurans
Bartonella henselae Houston-1 
Bradyrhizobium japonicum
Bacillus licheniformis ATCC 14580
Bifidobacterium longum
Burkholderia mallei ATCC 23344
Brucella melitensis
Bordetella parapertussis 12822
Bordetella pertussis Tohama I
Burkholderia pseudomallei K96243
Bartonella quintana Toulouse
Bacillus subtilis
Brucella suis 1330
Bacteroides thetaiotaomicron VPI-5482
Bacillus thuringiensis konkukian
Buchnera sp. APS
Clostridium acetobutylicum
Coxiella burnetii
Chlamydophila caviae
Caulobacter crescentus
Corynebacterium diphtheriae NCTC 13129
Corynebacterium efficiens YS-314
Corynebacterium glutamicum
Campylobacter jejuni
Campylobacter jejuni RM1221
Chlamydia muridarum
Clostridium perfringens
Clamydophila pneumoniae AR39
Chlorobium tepidum (TIGR)
Chlorobium tepidum TLS (NCBI)
Clostridium tetani E88
Clamydia trachomatis
Chromobacterium violaceum
Dehalococcoides ethenogenes 195
Desulfotalea psychrophila LSv54
Deinococcus radiodurans
Desulfovibrio vulgaris Hildenborough
Erwinia carotovora subsp. atroseptica SCRI1043
Escherichia coli
Escherichia coli O157:H7
Escherichia coli O157:H7 EDL933
uropathogenic E.coli
Enterococcus_faecalis_V583
Ehrlichia ruminantium str. Welgevonden 
Fusobacterium nucleatum
Francisella tularensis
Geobacillus kaustrophilus HTA426
Gluconobacter oxydans 621H
Geobacter sulfurreducens
Halobacterium sp.
Haemophilus ducreyi 35000HP
Helicobacter hepaticus
Haemophilus influenzae RD
Haloarcula marismortui ATCC 43049
Helicobacter pylori
Idiomarina loihiensis L2TR
Listeria innocua
Leptospira interrogans
Lactobacillus johnsonii NCC533
Lactococcus lactis
Listeria monocytogenes
Lactobacillus plantarum
Legionella pneumophila str. Lens
Leifsonia xyli CTCB0
Methanosarcina acetivorans C2A
Mycobacterium avium paratuberculosis
Mycobacterium bovis AF2122/97
Methylococcus capsulatus str. Bath
Mesoplasma florum L1
Mycoplasma gallisepticum R
Mycoplasma genitalium G-37
Mycoplasma hyopneumoniae 232
Methanococcus jannaschii
Methanopyrus kandleri
Mycobacterium leprae strain TN
Mezorhizobium loti 
Methanococcus maripaludis S2
Methanosarcina mazei
Mycoplasma mobile 163K
Mycoplasma mycoides subsp. mycoides SC str. PG1
Mycoplasma penetrans HF-2
Mycoplasma pneumoniae
Mycoplasma pulmonis UAB CTIP
Mannheimia succiniciproducens MBEL55E
Methanobacterium thermoautotrophicum
Mycobacterium tuberculosis H37Rv
Mycobacterium tuberculosis CDC1551
Nanoarchaeum equitans
Nitrosomonas europaea
Nocardia farcinica IFM 10152
Neisseria meningitidis MC58
Oceanobacillus iheyensis
Onion yellows phytoplasma OY-M
Pyrobaculum aerophilum 
Pyrococcus abysii
Propionibacterium acnes KPA171202
Pseudomonas aeruginosa
Parachlamydia sp. UWE25
Pyrococcus furiosus
Porphyromonas gingivalis W83
Pyrococcus horikoshii
Pirellula sp.
Photorhabdus luminescens subsp. laumondii TTO1
Pasteurella multocida
Photobacterium profundum SS9
Pseudomonas putida KT2440
Pseudomonas syringae
Picrophilus torridus
Rhodopirellula baltica SH 1
Rickettsia conorii
Rickettsia prowazekii
Ralstonia solanacearum GMI1000
Rickettsia typhi str. Wilmington
Streptococcus_agalactiae_2603
Staphylococcus aureus
Streptomyces avermitilis MA-4680
Streptomyces coelicolor
Staphylococcus_epidermidis_ATCC_12228
Shigella flexneri 2a str. 2457T
Sinorhizobium meliloti 
Streptococcus_mutans
Shewanella oneidensis
Streptococcus_pneumoniae_R6
Silicibacter pomeroyi DSS-3
Streptococcus pyogenes
Sulfolobus solfataricus
Streptococcus thermophilus CNRZ1066
Salmonella typhimurium
Thermoplasma acidophilum
Treponema denticola ATCC 35405
Thermococcus kodakaraensis
Thermotoga maritima
Treponema pallidum
Thermoanaerobacter tengcongensis
Thermus thermophilus HB27
Thermus thermophilus HB8
Thermoplasma volcanium 
Tropheryma whipplei TW08_27
Ureaplasma urealyticum
Vibrio cholerae
Vibrio vulnificus CMCP6
Wigglesworthia brevipalpis
Xanthomonas campestris
Xanthomonas citri
Xylella fastidiosa
Yersinia pestis CO92
Yersinia pestis KIM
Yersinia pestis biovar Medievalis str. 91001
Yersinia pseudotuberculosis IP 32953
Zymomonas mobilis subsp. mobilis ZM4