Table 4 Publicly available finished and unfinished genome sequence databases used in this study

Acidithiobacillus ferrooxidans

Escherichia coli O157:H7 EDL933

Rhodobacter sphaeroides

Actinobacillus actinomycetemcomitans

*Enterococcus faecalis

Salmonella dublin

Aquifex aeolicus

Geobacter sulfurreducens

Salmonella enteritidis

*Bacillus anthracis

Haemophilus ducreyi 35000HP

Salmonella paratyphi

*Bacillus halodurans

Haemophilus influenzae Rd

Salmonella typhi

*Bacillus subtilis

Helicobacter pylori 26695

Salmonella typhimurium LT2

*Bacillus stearothermophilus

Helicobacter pylori J99

Shewanella putrefaciens

Bordetella bronchiseptica

Klebsiella pneumoniae

Sinorhizobium meliloti

Bordetella parapertussis

*Lactococcus lactis subsp. lactis

*Staphylococcus aureus COL

Bordetella pertussis

Legionella pneumophila

*Staphylococcus aureus MRSA

Borrelia burgdorferi

*Listeria monocytogenes

*Staphylococcus aureus MSSA

Brucella melitensis biovar Suis

Mesorhizobium loti

*Staphylococcus aureus Mu50

Buchnera sp. APS

Methylococcus capsulatus

*Staphylococcus aureus N315

Burkholderia mallei

*Mycobacterium avium

*Staphylococcus aureus NCTC 8325

Burkholderia pseudomallei

*Mycobacterium avium subsp. paratuberculosis

*Staphylococcus epidermidis

Campylobacter jejuni NCTC 11168

*Mycobacterium bovis

*Streptococcus equi

Carboxydothermus hydrogenoformans

* Mycobacterium leprae

*Streptococcus gordonii

Caulobacter crescentus

*Mycobacterium smegmatis

*Streptococcus mutans

Chlamydia muridarum

*Mycobacterium tuberculosis 210

*Streptococcus pneumoniae

Chlamydia pneumoniae

*Mycobacterium tuberculosis CDC1551

*Streptococcus pyogenes

Chlamydia trachomatis D/UW-3/CX

*Mycobacterium tuberculosis H37Rv

Chlamydophila pneumoniae AR39

*Mycoplasma genitalium G37

*Streptococcus pyogenes Manfredo

Chlamydophila psittaci

*Mycoplasma pneumoniae M129

*Streptomyces coelicolor A3(2)

Chlorobium tepidum

Neisseria gonorrhoeae

Synechocystis PCC6803

*Clostridium acetobutylicum

Neisseria meningitidis MC58

Thermotoga maritima

*Clostridium difficile

Neisseria meningitidis Z2491

Treponema denticola

*Corynebacterium diphtheriae

Pasteurella multocida PM70

Treponema pallidum

Coxiella burnetii

Porphyromonas gingivalis W83

*Ureaplasma urealyticum

Dehalococcoides ethenogenes

Pseudomonas aeruginosa

Vibrio cholerae

Desulfovibrio vulgaris

Pseudomonas putida KT2440

Wolbachia

Deinococcus radiodurans

Pseudomonas putida PRS1

Xylella fastidiosa

Escherichia coli K-12 MG1655

Pseudomonas syringae pv. tomato

Yersinia enterocolitica

Escherichia coli O157:H7

Rickettsia prowazekii

Yersinia pestis