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Table 2 Analysis of select fGIs from the A. baumannii pan-chromosome

From: A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii

fGR

Functional categories

     

Region number+

End5

End3

Span (bp)

Number of fGIs

RI

GI

Phage

Metabolic

House-keeping

Extracellular polysaccharide

Description of largest fGI-encoded functions£

pAICU

Flanking core ACICU loci

fGR id

Largest fGI assemblies§

K

68497

82812

14316

17

     

X

K-antigen

1

00074/00087

CL_INS_4

105

N

152392

155346

2955

3

X

     

Novel; acetyltransferase, fragment of composite IS26 transposon

-

00139 (acylCS)/00147

CL_INS_12

791*

1

243163

350187

107025

38

X

     

comM, aminoglycoside/hydroxyurea antibiotic resistance kinase, streptomycin 3″-kinase, transporter, major facilitator family protein

3

00219/00242

CL_INS_20

58*

2

702940

747393

44454

7

 

X

    

Copper/heavy metal resistance

-

00567/00568

CL_INS_49

16

3

906910

938373

31464

9

 

X

    

Phage 1 in ACICU, but no core phage genes

6

00684/00702

CL_INS_65

64

4

1103071

1189920

86850

62

  

X

   

Toxin/anti-toxin system, large terminase, methylase

-

00861/00869

CL_INS_74

9

5

1401709

1425417

23709

43

  

X

   

phage protein F-like

-

01048/01056

CL_INS_93

29

6

1425814

1449657

23844

31

  

X

   

Arc-like protein, lysozyme

  

CL_INS_94

76

7

1472644

1510578

37935

16

  

X

   

Major capsid, prohead protease, portal, large and small terminase, head-tail adaptor, tail protein, lysozyme, antitermination protein Q, integrase

  

CL_INS_97

14

8

1561693

1595358

33666

11

 

X

    

Zeta toxin, phage/plasmid-like protein, recombinase

-

01106/01110

CL_INS_101

52

9

1603966

1639890

35925

2

   

X

  

bla, hlyD, phenylpropanoid catabolism, porin, acetaldehyde dehydrogenase; ompA-like, yadA-like

-

01115/01116

CL_INS_104

38, 260*

10

1666240

1704336

38097

7

   

X

  

Aldehyde dehydrogenase, vanillin dehydrogenase, porins, transporters

-

01136 (astA)/01153

CL_INS_107

28

11

1818532

1852125

33594

12

  

X

   

Lysis protein, tail, tail assembly, tape measure

-

01222/01224

CL_INS_120

50

12

1928539

1956234

27696

2

   

X

  

bla, hlyD, phenylpropanoid catabolism, porin, acetaldehyde dehydrogenase

-

01256/01257

CL_INS_128

38

13

2402650

2440626

37977

32

  

X

   

Major capsid, prohead protease, portal, large and small terminase, head-tail adaptor, tail protein, lysozyme, antitermination protein Q, integrase

-

01626/01627

CL_INS_164

14

14

2664622

2705871

41250

11

  

X

   

Inovirus-like; zonula occludens toxin, coat protein B, replication protein

-

01813/01815

CL_INS_180

110

15

2716186

2754267

38082

6

 

X

  

X

 

tatABC, TonB receptors, ABC transporters

-

01824/01827

CL_INS_182

33

16

2802271

2828589

26319

15

  

X

   

Phage-associated protein, phage protein F-like, site-specific recombinase

-

01849/01864

CL_INS_187

40

17

2850997

2872608

21612

2

   

X

  

Oxidoreductase, aldehyde dehydrogenase

-

01886/01887

CL_INS_190

62

18

2874184

2899845

25662

2

   

X

X

 

tRNA ligase, aldehyde dehydrogenases, Homoprotocatechuate/hydroxyphenylacetate degradation, transporter

-

01887/01888

CL_INS_191

37

19

2990911

3011439

20529

4

   

X

  

Medium chain fatty acid ligase, transporter, oxidoreductase

-

01936/01949

CL_INS_199

121

20

3143872

3176853

32982

7

  

X

   

Mu-like; Gam-like protein, terminase, methylase, Mu protein F-like, Mu-like major head, tail sheath-like, Mu Gp45, baseplate J-like

-

02064/02066

CL_INS_211

15

21

3250042

3277383

27342

12

  

X

   

lysozyme, baseplate, phage protein F-like, phage-associated protein

-

02139/02236

CL_INS_216

25

22

3465244

3487854

22611

3

 

X

    

Novel 7.8 kb region; salicylate monooxygenase

-

02398/02399 (acetylT)

CL_INS_237

338*

23

3569029

3597828

28800

6

  

X

   

Phage

-

02457/02470

CL_INS_246

19

24

3790117

3828819

38703

12

   

X

  

Rubredoxin, MFS transporter, prevent host death, aldehyde dehydrogenase, methylmalonate-semialdehyde dehydrogenase

29

02595/02624

CL_INS_259

35

25

4223758

4247211

23454

6

  

X

   

Integrase, CII, large and small terminase, portal, prohead protease, major capsid, head-tail connector, head-tail joining, tail

-

03014/03015

CL_INS_287

59

O

4387696

4395870

8175

5

     

X

O-antigen

-

03146/03149

CL_INS_297

168

26

4420246

4450038

29793

6

  

X

   

P2-like; integrase, tape measure, tail proteins, baseplate J-like, lysozyme, baseplate assembly, large and small terminase, major capsid, capsid scaffolding protein, portal

-

03157/03161

CL_INS_299

17

27

4818799

4844895

26097

2

X

   

X

 

Novel; bla, Tn7, sulfur transport, fur, tRNA ligase

-

03502/03503

CL_INS_334

39

28

4960555

4989495

28941

5

 

X

    

ompA-like protein, Tnp

-

03594/03595

CL_INS_346

148

  1. +Cross reference with Fig. 4B
  2. £Only functions from select fGIs are listed. Other elements and functions may be encoded within selected fGRs
  3. Not all fGIs are present in ACICU
  4. Largest fGI in fGR similar in composition to the “alien islands” reported by Iacono et al. [38]
  5. Cross reference Additional files 5 and 21
  6. §Cross reference Additional files 18 and 21
  7. *Not largest fGI in region