Table 1 Species used in the current work and their accession numbers

Agrobacterium tumefaciens str. C58 (Cereon)

NC_003062

2,841,581

Agrobacterium tumefaciens str. C58 (U. Washington)

NC_003304

2,841,490

Aquifex aeolicus VF5

NC_000918

1,551,335

Bacillus anthracis str. Ames

NC_003997

5,227,293

Bacillus cereus ATCC 14579

NC_004722

5,411,809

Bacillus halodurans

NC_002570

4,202,353

Bacillus subtilis subsp. subtilis str. 168

NC_000964

4,214,814

Bacteroides thetaiotaomicron VPI-5482

NC_004663

6,260,361

Bifidobacterium longum NCC2705

NC_004307

2,256,646

Bordetella bronchiseptica

NC_002927

5,339,179

Bordetella parapertussis

NC_002928

4,773,551

Bordetella pertussis

NC_002929

4,086,189

Borrelia burgdorferi B31

NC_001318

910,724

Bradyrhizobium japonicum USDA 110

NC_004463

9,105,828

Brucella melitensis 16M

NC_003317

2,117,144

Brucella suis 1330

NC_004310

2,107,792

Buchnera aphidicola str. APS (Acyrthosiphon pisum)

NC_002528

640,681

Buchnera aphidicola str. Bp (Baizongia pistaciae)

NC_004545

615,980

Buchnera aphidicola str. Sg (Schizaphis graminum)

NC_004061

641,454

Campylobacter jejuni subsp. jejuni NCTC 11168

NC_002163

1,641,481

Candidatus Blochmannia floridanus

NC_005061

705,557

Caulobacter crescentus CB15

NC_002696

4,016,947

Chlamydia muridarum

NC_002620

1,072,950

Chlamydia trachomatis

NC_000117

1,042,519

Chlamydophila caviae GPIC

NC_003361

1,173,390

Chlamydophila pneumoniae AR39

NC_002179

1,229,858

Chlamydophila pneumoniae CWL029

NC_000922

1,230,230

Chlamydophila pneumoniae J138

NC_002491

1,226,565

Chlamydophila pneumoniae TW-183

NC_005043

1,225,935

Chlorobium tepidum TLS

NC_002932

2,154,946

Chromobacterium violaceum ATCC 12472

NC_005085

4,751,080

Clostridium acetobutylicum

NC_003030

3,940,880

Clostridium perfringens str. 13

NC_003366

3,031,430

Clostridium tetani E88

NC_004557

2,799,251

Corynebacterium diphtheriae

NC_002935

2,488,635

Corynebacterium efficiens YS-314

NC_004369

3,147,090

Corynebacterium glutamicum ATCC 13032

NC_003450

3,309,401

Coxiella burnetii RSA 493

NC_002971

1,995,275

Deinococcus radiodurans

NC_001263

2,648,638

Enterococcus faecalis V583

NC_004668

3,218,031

Escherichia coli CFT073

NC_004431

5,231,428

Escherichia coli K12

NC_000913

4,639,221

Escherichia coli O157:H7

NC_002695

5,498,450

Escherichia coli O157:H7 EDL933

NC_002655

5,528,445

Fusobacterium nucleatum subsp. nucleatum ATCC 25586

NC_003454

2,174,500

Gloeobacter violaceus

NC_005125

4,659,019

Haemophilus ducreyi 35000HP

NC_002940

1,698,955

Haemophilus influenzae Rd

NC_000907

1,830,138

Helicobacter hepaticus ATCC 51449

NC_004917

1,799,146

Helicobacter pylori 26695

NC_000915

1,667,867

Helicobacter pylori J99

NC_000921

1,643,831

Lactobacillus plantarum WCFS1

NC_004567

3,308,274

Lactococcus lactis subsp. lactis

NC_002662

2,365,589

Leptospira interrogans serovar lai str. 56601

NC_004342

4,332,241

Listeria innocua

NC_003212

3,011,208

Listeria monocytogenes EGD-e

NC_003210

2,944,528

Mesorhizobium loti

NC_002678

7,036,074

Mycobacterium bovis subsp. bovis AF2122/97

NC_002945

4,345,492

Mycobacterium leprae

NC_002677

3,268,203

Mycobacterium tuberculosis CDC1551

NC_002755

4,403,836

Mycobacterium tuberculosis H37Rv

NC_000962

4,411,529

Mycoplasma gallisepticum R

NC_004829

996,422

Mycoplasma genitalium

NC_000908

580,074

Mycoplasma penetrans

NC_004432

1,358,633

Mycoplasma pneumoniae

NC_000912

816,394

Mycoplasma pulmonis

NC_002771

963,879

Neisseria meningitidis MC58

NC_003112

2,272,351

Neisseria meningitidis Z2491

NC_003116

2,184,406

Nitrosomonas europaea ATCC 19718

NC_004757

2,812,094

Nostoc sp. PCC 7120

NC_003272

6,413,771

Oceanobacillus iheyensis HTE831

NC_004193

3,630,528

Pasteurella multocida

NC_002663

2,257,487

Photorhabdus luminescens subsp. laumondii TTO1

NC_005126

5,688,987

Pirellula sp.

NC_005027

7,145,576

Porphyromonas gingivalis W83

NC_002950

2,343,476

Prochlorococcus marinus str. MIT 9313

NC_005071

2,410,873

Prochlorococcus marinus subsp. marinus str. CCMP1375

NC_005042

1,751,080

Prochlorococcus marinus subsp. pastoris str. CCMP1378

NC_005072

1,657,990

Pseudomonas aeruginosa PA01

NC_002516

6,264,403

Pseudomonas putida KT2440

NC_002947

6,181,863

Pseudomonas syringae pv. tomato str. DC3000

NC_004578

6,397,126

Ralstonia solanacearum

NC_003295

3,716,413

Rickettsia conorii

NC_003103

1,268,755

Rickettsia prowazekii

NC_000963

1,111,523

Salmonella enterica subsp. enterica serovar Typhi

NC_003198

4,809,037

Salmonella enterica subsp. enterica serovar Typhi Ty2

NC_004631

4,791,961

Salmonella typhimurium LT2

NC_003197

4,857,432

Shewanella oneidensis MR-1

NC_004347

4,969,803

Shigella flexneri 2a str. 2457T

NC_004741

4,599,354

Shigella flexneri 2a str. 301

NC_004337

4,607,203

Sinorhizobium meliloti

NC_003047

3,654,135

Staphylococcus aureus subsp. aureus MW2

NC_003923

2,820,462

Staphylococcus aureus subsp. aureus Mu50

NC_002758

2,878,040

Staphylococcus aureus subsp. aureus N315

NC_002745

2,814,816

Staphylococcus epidermidis ATCC 12228

NC_004461

2,499,279

Streptococcus agalactiae 2603V/R

NC_004116

2,160,267

Streptococcus agalactiae NEM316

NC_004368

211,485

Streptococcus mutans UA159

NC_004350

203,0921

Streptococcus pneumoniae R6

NC_003098

2,038,615

Streptococcus pneumoniae TIGR4

NC_003028

2,160,837

Streptococcus pyogenes M1 GAS

NC_002737

1,852,441

Streptococcus pyogenes MGAS315

NC_004070

1,900,521

Streptococcus pyogenes MGAS8232

NC_003485

1,895,017

Streptococcus pyogenes SSI-1

NC_004606

1,894,275

Streptomyces avermitilis MA-4680

NC_003155

9,025,608

Streptomyces coelicolor A3(2)

NC_003888

8,667,507

Synechococcus sp. WH 8102

NC_005070

2,434,428

Synechocystis sp. PCC 6803

NC_000911

3,573,470

Thermoanaerobacter tengcongensis

NC_003869

2,689,445

Thermosynechococcus elongates BP-1

NC_004113

2,593,857

Thermotoga maritima

NC_000853

1,860,725

Treponema pallidum

NC_000919

1,138,011

Tropheryma whipplei TW08/27

NC_004551

925,938

Tropheryma whipplei str. Twist

NC_004572

927,303

Ureaplasma urealyticum

NC_002162

751,719

Vibrio cholerae

NC_002505

2,961,149

Vibrio parahaemolyticus RIMD 2210633

NC_004603

3,288,558

Vibrio vulnificus CMCP6

NC_004459

3,281,945

Vibrio vulnificus YJ016

NC_005139

3,354,505

Wigglesworthia glossinidia (from Glossina brevipalpis)

NC_004344

697,724

Wolinella succinogenes

NC_005090

2,110,355

Xanthomonas axonopodis pv. citri str. 306

NC_003919

5,175,554

Xanthomonas campestris pv. campestris str. ATCC 33913

NC_003902

5,076,188

Xylella fastidiosa 9a5c

NC_002488

2,679,306

Xylella fastidiosa Temecula1

NC_004556

2,519,802

Yersinia pestis CO92

NC_003143

4,653,728

Yersinia pestis KIM

NC_004088

4,600,755