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Table 1 Summary of the 48 bacterial genomes used in this study and the PAS/PDC domains identified

From: Reductive evolution and the loss of PDC/PAS domains from the genus Staphylococcus

Speciesa

Subspecies/strain

Accession number

Phylum

Pathogenicityb

Motilityc

Total proteinsd

PDC/PAS proteinse

PAS domainsf

PDC domainsg

[Gram positive]

         

Bifidobacterium animalis

lactis AD011

NC_011835.1

Actinobacteria

0

0

1527

5

4

2

Corynebacterium diphtheriae (Ci)

NCTC 13129

NC_002935.2

Actinobacteria

1

0

2272

4

2

2

Corynebacterium glutamicum (Cg)

ATCC 13032

NC_006958.1

Actinobacteria

0

0

3057

7

5

4

Micrococcus luteus (Ml)

NCTC 2665

NC_012803.1

Actinobacteria

0

0

2236

5

4

3

Mycobacterium leprae

TN

NC_002677.1

Actinobacteria

1

0

1605

6

7

1

Mycobacterium smegmatis (Ms)

MC2 155

NC_008596.1

Actinobacteria

0

0

6717

20

17

10

Mycobacterium tuberculosis (Mt)

CDC1551

NC_002755.2

Actinobacteria

1

0

4189

10

6

7

Streptomyces coelicolor (Stc)

A3(2)

NC_003888.3

Actinobacteria

0

0

8154

51

48

18

Bacillus anthracis (Ba)

CDC 684

NC_012581.1

Firmicutes

1

0

5902

43

30

30

Bacillus cereus (Bc)

ATCC 10987

NC_003909.8

Firmicutes

1

1

5843

41

30

25

Bacillus megaterium (Bm)

QM B1551

NC_010010.2

Firmicutes

0

1

5612

53

57

21

Bacillus subtilis (Bs)

subtilis 168

NC_000964.3

Firmicutes

0

1

4176

32

21

30

Clostridium acetobutylicum (Ca)

ATCC 824

NC_003030.1

Firmicutes

0

1

3847

36

16

34

Clostridium botulinum

A str. ATCC 3502

NC_009496.1

Firmicutes

1

1

3590

48

31

40

Clostridium difficile (Cd)

630

NC_009089.1

Firmicutes

1

1

3749

49

49

26

Enterococcus faecalis (Efs)

V583

NC_004668.1

Firmicutes

1

0

3264

9

7

7

Enterococcus faecium (Efm)

DO

NZ_AAAK00000000

Firmicutes

1

0

3114

9

3

10

Lactobacillus casei (Lc)

ATCC 334

NC_008526.1

Firmicutes

0

0

2768

8

6

4

Lactococcus lactis (Ll)

cremoris MG1363

NC_009004.1

Firmicutes

0

0

2434

5

5

0

Listeria monocytogenes (Lm)

EGD-e

NP_463535.1

Firmicutes

1

1

2846

12

9

7

Macrococcus caseolyticus (Mc)

JCSC5402

NC_011999.1

Firmicutes

0

0

2052

7

6

4

Staphylococcus aureus (SaU)

aureus USA300_TCH1516

NC_010079.1

Firmicutes

1

0

2693

8

5

7

Staphylococcus aureus (SaC)

aureus COL

NC_002951.2

Firmicutes

1

0

2612

8

5

7

Staphylococcus carnosus (Sc)

carnosus TM300

NC_012121.1

Firmicutes

0

0

2461

9

8

5

Staphylococcus epidermidis (Se)

ATCC 12228

NC_004461.1

Firmicutes

1

0

2416

8

5

7

Staphylococcus haemolyticus (Sh)

JCSC1435

NC_007168.1

Firmicutes

1

0

2676

7

5

4h

Staphylococcus lugdunensis (Sl)

HKU09-01

CP_001837.1

Firmicutes

1

0

2490

7

5

5

Staphylococcus pseudintermedius (Sp)

HKU10-03

NC_014925.1

Firmicutes

1

0

2450

8

5

7

Staphylococcus saprophyticus (Ss)

saprophyticus ATCC15305

NC_007350.1

Firmicutes

1

0

2446

6

4

5

Streptococcus agalactiae

2603 V/R

NC_004116.1

Firmicutes

1

0

2124

11

6

7

Streptococcus pneumoniae (Spn)

D39

NC_008533.1

Firmicutes

1

0

1914

8

5

4

Streptococcus pyogenes (Spy)

MGAS10270

NC_008022.1

Firmicutes

1

0

1986

11

4

10

[Gram negative]

         

Nostoc punctiforme

PCC 73102

NC_010628.1

Cyanobacteria

0

1

6689

97

131

38

Synechococcus sp

CC9311

NC_008319.1

Cyanobacteria

0

1

2892

12

8

6

Agrobacterium tumefaciens

C58

NC_003062.2

Proteobacteria

0

1

5355

63

61

27

Bartonella henselae

Houston-1

NC_005956.1

Proteobacteria

1

0

1488

8

10

2

Bradyrhizobium sp

BTAi1

NC_009485.1

Proteobacteria

0

1

7621

98

103

51

Escherichia coli (Ec)

K-12 substr. MG1655

NC_000913.2

Proteobacteria

0

1

4146

32

24

18

Helicobacter pylori

83

CP002605.1

Proteobacteria

1

1

1609

5

1

7

Klebsiella pneumoniae (Kp)

342

NC_011283.1

Proteobacteria

1

0

5768

33

24

18

Neisseria meningitidis

MC58

NC_003112.1

Proteobacteria

1

0

2063

3

2

1

Pseudomonas aeruginosa

PAO1

NC_002516.1

Proteobacteria

1

1

5571

70

71

35

Salmonella enterica

arizonae serovar

NC_010067.1

Proteobacteria

1

1

4500

21

12

13

Shigella flexneri

2a str. 2457 T

NC_004741.1

Proteobacteria

1

0

4060

18

11

9

Vibrio cholerae

MJ-1236

NC_012668.1

Proteobacteria

1

1

3772

71

42

59

Yersinia pestis

CO92

NC_003143.1

Proteobacteria

1

1

4066

20

10

13

Leptospira biflexa

serovar Patoc

CP000788.1

Spirochaetes

0

1

3726

67

76

30

Treponema pallidum

pallidum SS14

CP000805.1

Spirochaetes

1

1

1028

5

1

6

  1. aFor those included in our phylogenetic analysis, abbreviations for species names are shown in parentheses.
  2. b1: pathogenic, 0: non-pathogenic.
  3. c1: motile, 0: non-motile.
  4. dTotal number of proteins in the genome.
  5. eTotal number of PAS/PDC-containing proteins identified in the genome.
  6. fTotal number of PAS domains identified.
  7. gTotal number of PDC domains identified.
  8. hOne of the PDC/PAS-containing proteins in Staphylococcus haemolyticus (Sh.3, YP_253148.1, PhoR) does not have the PDC domain identified by HHblits nor HHsearch, although all other Staphylococcus PhoR homologs have clearly identified PDC domains. However, as noted in Supplementary Table S1, a very weakly conserved PDC-like region was identified in this protein based on the predicted secondary structure. This potential PDC domain is not included in this table nor in our analysis.
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BMC Genomics

ISSN: 1471-2164

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