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Table 2 Previously characterized and potential new TAS components detected with the second approach

From: Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes

Query family

Source

Adjacent gene family

Adjacent gene function; reasons if discarded.

Number of occurrences observed

AbrB/MazE

[3]

PIN

Nuclease

312

  

MazF

RNA interferase

97

  

Fic/Doc

AMPylation enzyme

48

  

RelE

RNA interferase

27

ArsR

Table 1

COG3832

Aha1 domain

280

  

COG0394*

Arsenate reductase arsC; Part of a larger conserved gene associations

98

  

COG2217*

Cation transport ATPase; Part of a larger conserved gene associations

83

  

COG0798*

Arsenite efflux pump ACR3; Part of a larger conserved gene associations

74

  

COG2391*

YeeE/YedE family, DUF395; Part of a larger conserved gene associations

64

  

COG1055*

Arsenical pump membrane protein; Part of a larger conserved gene associations

53

RHH

[3]

RelE

RNA interferase

376

  

PIN

Nuclease

335

  

GNAT

Acetyltransferase

139

  

MazF

RNA interferase

62

  

COG3505*

TraG/TraD/VirD4 family; Part of a larger conserved gene associations

58

  

COG2929

DUF497

55

  

ParA*

ParA, plasmid partitioning ATPase; Part of a larger conserved gene associations

54

  

HicA

RNA interferase

26

  

RHH

DNA-binding domain

23

  

COG0716*

Flavodoxin; Part of a larger conserved gene associations

22

  

COG4962*

Type II/IV secretion system protein; Part of a larger conserved gene associations

21

Fic_Doc

[3]

AbrB

DNA-binding domain

55

  

xre

DNA-binding domain

22

  

yhfG

Unknown

11

MazF

[3]

AbrB

DNA-binding domain

107

  

RHH

DNA-binding domain

81

  

MazF/ccd

RNA interferase

43

  

XF1863

Unknown

29

RelE

[3]

xre

Transcriptional regulator

730

  

RHH

DNA-binding domain

510

  

PHD

DNA-binding domain

337

  

COG2856

Zn peptidase (fused to HTH)

15

  

COG1753

Predicted DNA-binding domain; RHH fold

10

PIN

RNA nuclease

[3]

RHH

DNA-binding domain

366

  

AbrB

DNA-binding domain

348

  

PHD

DNA-binding domain

285

  

COG2442

Protein of unknown function DUF433

97

  

COG2886

Uncharacterized protein family (UPF0175)

46

  

COG2856

Zn peptidase (fused to HTH)

42

  

MazF/ccd

COG5302

41

  

COG1211*

4-diphosphocytidyl-2-methyl-D-erithritol synthase; Part of a larger conserved gene associations

39

  

MerR

Transcriptional regulator

33

  

COG1066*

Sms; Part of a large conserved gene associations

26

  

COG1092*

SAM-dependent methyltransferase; Part of a larger conserved gene associations

26

  

COG2880

Predicted DNA-binding protein; AbrB superfamily

24

  

pfam00155*

Aminotransferase; Part of a larger conserved gene associations

24

  

COG5257*

Translation initiation factor 2; Part of a larger conserved gene associations

20

  

COG1753

Predicted DNA-binding domain; RHH fold

20

PHD

[3]

PIN

Nuclease

276

  

SMa0917

PemK/MazFI

15

MNT

Table 1

HEPN

Unknown

445

HEPN

Table 1

MNT

Predicted nucleotidyltransferase

482

Xre

[3]

RelE

RNA interferase

614

  

HipA

EF-Tu kinase

244

  

COG2856

Zincin protease

194

  

xre

A variety of proteins containing xre-like HTH, many fused with various domain, not a distinct set

97

  

PIN

Nuclease

67

  

DUF397

Unknown

64

  

COG0800*

2-keto-3-deoxy-6-phosphogluconate aldolase; Part of a larger conserved gene associations

46

  

COG3842*

PotA is ABC-type transporter; Part of a larger conserved gene associations

40

  

PA2784-like*

A membrane protein, likely an exporter

36

  

YoaS-like*

A membrane protein, likely permease

32

  

antirepressor

BRO family; KilA – letal to host cells

30

  

GNAT

Acetyltransferase

30

  

COG3063*

Tfp pilus assembly protein PilF; Part of a large conserved gene associations

27

  

PA4076-like*

A membrane protein, likely an exporter

27

  

COG4974*

Site-specific recombinase XerD; Apparent phage components with another function

25

  

COG0483*

Archaeal fructose-1,6-bisphosphatase; Part of a larger conserved gene associations

21

xre COG5642 subfamily

 

COG5654

Predicted transcriptional regulator

118

HipA

[3]

xre

Transcriptional regulator

333

  

COG3550

HipA C-terminal

51

COG2856

[60]

xre

Transcriptional regulator

145

  

PIN

Nuclease

60

  

RelE

RNA interferase

22

COG2880

[13]

PIN

Nuclease

25

COG3832

Table 1

ArsR

Transcriptional regulator

259

COG4636

[13]

COG4636

Predicted endonuclease

114

COG4679 (RelE family)

[13]

COG5606

Predicted RNA interferase

43

  1. New TAS discussed in this work are shown in bold type; other associations marked by asterisk in column 3 were disregarded for reasons indicated in column 4.