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Table 1 Significant HPTs in B. pertussis, B. bronchiseptica, and B. Parapertussis

From: Phase variation and microevolution at homopolymeric tracts in Bordetella pertussis

 

B. pertussis Tohama I

B. bronchiseptica RB50

B. parapertussis 12822

      

HPTa

ORFb

Allelec

ORF

Allele

ORF

Allele

Gene

Base

Poly-morphicd

Loce

Promoter overlapf

Functional categoryg

11

BP2991

7

BB4384

9

BPP3911

9

 

A/T

y

I

L

Biosynthesis of cofactors, carriers

12

BP3682

8

BB0097

8

BPP0098

8

 

A/T

n

I

M

Hypothetical protein

13

  

BB0618, BB0619

8

BPP0612, BPP0613

7

 

A/T

y

I

H

Global regulatory functions

14

  

BB0622

8

BPP0616

8

 

A/T

n

I

M

Conserved hypothetical

15

BP3151

9

BB0875

8

BPP0790

8

 

A/T

y

I

L

Cell envelope

16

  

BB0999

8

BPP0906

8

 

A/T

n

I

L

Transport/binding proteins

17

BP0880

7

BB1564

8

BPP2167

7

 

A/T

y

I

L

Periplasmic/exported/lipoproteins

18

BP2792

8

BB1918

8

BPP2471

8

 

A/T

n

I

H

Hypothetical protein

19

BP2908

8

BB1935

8

BPP2488

8

aroG

A/T

n

I

L

Amino acid biosynthesis

20

BP2735

8

BB2036

8

BPP2594

8

 

A/T

n

I

H

Conserved hypothetical

21

BP2539

8

BB2083

8

BPP2640

8

 

A/T

n

I

L

Cell envelope

23

BP1487

8

BB2136

8

BPP1948

8

smoM h

A/T

n

I

M

Transport/binding proteins

24

BP1419

8

BB2605

8

BPP1527

8

rpsB

A/T

n

I

M

Ribosome constituents

25

BP1245

9

BB3248

8

BPP1860

11

 

A/T

y

I

M

Conserved hypothetical

26

BP1231

8

BB3262

8

BPP1846

8

 

A/T

n

I

H

Cell envelope

27

BP2399

8

BB3715

8

BPP3264

7

 

A/T

y

I

L

Global regulatory functions

28

BP2425

8

BB3740

8

BPP3289

9

 

A/T

y

I

M

Periplasmic/exported/lipoproteins

29

BP0858

9

BB3824

8

BPP3373

9

 

A/T

y

I

H

Hypothetical protein

30

BP0856

8

BB3826

8

BPP3376

10

bfrD

A/T

y

I

L

Adaptation

31

BP3399

8

BB3987

8

BPP3552

8

 

A/T

n

I

M

Conserved hypothetical

32

  

BB4499

8

BPP4026

8

 

A/T

y

I

H

Conserved hypothetical

33

BP0347

8

BB4655

8

BPP4185

8

bhuR

A/T

n

I

K

Adaptation

34

BP3870

8

BB5012

8

BPP4424

8

 

A/T

n

I

M

Hypothetical protein

41

BP2506, BP2507

9

BB3941, BB3942

9

BPP3494

9

 

A/T

n

I

N

Macromolecule synthesis, modification

43

BP2863

9

BB1178

9

BPP0966

9

 

A/T

n

I

H

Conserved hypothetical

50

BP0939

8

     

A/T

y

I

L

Conserved hypothetical

51

BP0964

8

BB3455

9

BPP3115

9

 

A/T

y

I

L

Hypothetical protein

52

BP0966

8

BB3453

9

BPP1655

9

sbp

A/T

y

I

M

Transport/binding proteins

56

BP2936

8

BB1280

8

BPP1064

9

 

A/T

y

I

M

Periplasmic/exported/lipoproteins

60

BP0598

6

BB0289

6

BPP0286

8

 

A/T

y

I

L

Conserved hypothetical

64

  

BB1238

7

BPP1024

8

 

A/T

y

I

M

Energy metabolism, carbon

68

BP2084

7

BB3340

7

BPP1768

8

 

A/T

y

I

H

Conserved hypothetical

69

BP1811

6

BB3216

6

BPP1892

8

kdgT

A/T

y

I

M

Transport/binding proteins

70

BP1781

6

BB2260

7

BPP2012

8

 

A/T

y

C

 

Conserved hypothetical

73

    

BPP2251

8

bapA

A/T

y

I

L

Cell envelope

76

BP1893, BP1894i

A2CA6

BB2980, BB2979i

A2CA6

BPP3014, BPP3013i

9

 

A/T

y

I

H

Cons. hypo.; Global reg. functions

79

BP3852

nrj

BB4994

7

BPP4406

8

katA

A/T

y

I

L

Protection responses

83

  

BB3111, BB3112i

8

BPP1616, BPP1617i

8

 

A/T

n

I

L

Cell envelope; hypothetical protein

84

tRNA-Asn, tRNA-Thri

8

tRNA-Asn, tRNA-Thri

8

tRNA-Asn, tRNA-Thri

8

 

A/T

n

I

U

Macromolecule synthesis, modification

1

  

BB0357

11

BPP0354

8

 

C/G

y

I

M

Periplasmic/exported/lipoproteins

2

  

BB1186

10

BPP0974

7

 

C/G

y

I

M

Periplasmic/exported/lipoproteins

3

BP1568

13

BB1658

22

BPP2262

C6TC3

fim3

C/G

y

I

K

Cell envelope

4

BP2738

11

BB2033

7

BPP2591

7

bapC h

C/G

y

C

 

Cell envelope

5

  

BB3110

17

BPP1618

nr

 

C/G

y

C

 

Cell envelope

6

BP1201

9

BB3291

17

  

tcfA

C/G

y

C

 

Cell envelope

7

  

BB3425

15

BPP1683

10

fimN

C/G

y

I

K

Cell envelope

8

BP2674

7

BB3426

13

BPP1682

9

fimX

C/G

y

I

K

Cell envelope

9

BP1119

12

BB3674

20

BPP3222

C9TC8

fim2

C/G

y

I

K

Cell envelope

10

BP3037, BP3038

11

BB4210, BB4211

11

BPP3764, BPP3765

9

 

C/G

y

I

N

Hypothetical protein

22

BP1487

9

BB2136

C5GC3

BPP1948

C5GC3

smoM h

C/G

y

C

 

Transport/binding proteins

35

BP0146

15

BB4482

6

BPP4009

6

 

C/G

y

I

H

Hypothetical protein

36

BP1766

10

BB2245

G6TG3

BPP1997

8

 

C/G

y

I

N

Central intermediary metabolism

37

BP1879

10

BB2993

3

BPP3027

2

fhaB

C/G

y

C

 

Cell envelope

39

BP1961

11

BB1784

nr

BPP2333

nr

 

C/G

y

I

H

Energy metabolism, carbon

40

BP2483

10

BB3920

C2AC5

BPP3471

C2AC5

kdpD

C/G

y

C

 

Global regulatory functions

42

BP2595

12

BB2360

G3TG3

BPP1295

G3TG3

 

C/G

y

C

 

Macromolecule degradation

44

BP2896

9

BB1947

8

BPP2500

7

 

C/G

y

I

H

Hypothetical protein

45

BP3224

9

BB4011

6

BPP3576

nr

 

C/G

y

C

 

Energy metabolism, carbon

46

BP3474

13

BB0944

9

BPP0850

7

 

C/G

y

I

M

Conserved hypothetical

59

BP3624

7

BB0040

7

BPP0040

9

 

C/G

y

I

H

Degradation of small molecules

61

BP0520

6

BB0444

5

BPP0443

9

 

C/G

y

I

L

Periplasmic/exported/lipoproteins

62

BP0426

nr

BB0472

7

BPP0472

13

cspA

C/G

y

I

L

Adaptation

65

  

BB1351

9

BPP1135

9

 

C/G

n

I

H

Global regulatory functions

66

BP1047

7

BB1361

8

BPP1145

10

 

C/G

y

I

M

Periplasmic/exported/lipoproteins

67

BP1160

8

BB2684

8

BPP1607

11

 

C/G

y

C

 

Periplasmic/exported/lipoproteins

71

BP1793

2

BB2270

18

BPP2022

G12TG2AG3

 

C/G

y

I

L

Cell envelope

75

BP1660

G5CG2CG3

BB2741

8

BPP2745

12

sphB2

C/G

y

C

 

Cell envelope

78

  

BB4881

G4ACG2

BPP4294

14

 

C/G

y

I

H

Global regulatory functions

82

BP2738

14

BB2033

35

BPP2591

C6TC5

bapC h

C/G

y

C

 

Cell envelope

  1. a HPT number is an arbitrarily assigned unique ID. Table is sorted by order in the B. bronchiseptica RB50 genome.
  2. b Identifier of ORF that is either contains or is downstream of the HPT. Empty cell indicates that no orthologous sequence exists in that genome.
  3. c Numbers are length of HPTs. Sequences are given when the tract contains a substitution relative to alleles in the other genomes.
  4. d "y" denotes HPT length polymorphism among the three sequenced genomes.
  5. e "I", located in intergenic region; "C", located in coding sequence
  6. f Probability that the HPT overlaps a promoter coded as follows: H, high; M, moderate; L, low; N, not near a promoter (located in 3' region of convergently transcribed genes); K, known to overlap experimentally defined promoter; U, undetermined. Values were not assigned to coding HPTs. See Methods for definitions of classes.
  7. g Functional categories from MultiFun classification system as assigned by Parkhill, et al. [3]
  8. h Two separate HPTs are found in these genes.
  9. i HPT is upstream of two features by a similar distance.
  10. j "nr" indicates that no HPT is found in the orthologous region.
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BMC Genomics

ISSN: 1471-2164

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