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Table 1 List of PSSM profiles selected in TAcddb to verify the presence of a conserved TA-related domain

From: RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes

PSSMid

CD accession name

Relation/involvement in TA world

Reference

28977

cd00093-HTH_XRE

XRE-like domain present in HigA and VapB antitoxins

[20], this study

31586

COG1396-HipB

Involved in production of persister cells (antitoxin)

[20]

31676

COG1487-VapC

Quality control of gene expression

[57]

31786

COG1598

HicB of HicAB system (function undetermined)

[58]

31910

COG1724

HicA of HicAB system (function undetermined)

[58]

32033

COG1848

PIN domain, present in VapC toxins

[20,59,60]

32185

COG2002-AbrB

Domain present in of MazE and VapB antitoxins

[20]

32209

COG2026-RelE

Toxin of cytotoxic translational repressor system

[14,28,29]

32344

COG2161-StbD

Antitoxin of the RelBE family

[61]

32487

COG2336-MazE

Growth regulator (antitoxin)

[45]

32488

COG2337-MazF

Growth inhibitor (toxin)

[45]

32907

COG3093-VapI

Named from VapI region; corresponds to VapB antitoxins (Plasmid maintenance)

[62], this study

33351

COG3549-HigB

Toxin of plasmid maintenance system

[23]

33352

COG3550-HipA

Involved in production of persister cells (toxin)

[20]

33408

COG3609

CopG/Arc/MetJ DNA-binding domain, present in RelB, ParD, VapBCand CcdA antitoxins

[20], this study

33452

COG3654-Doc

Toxin of probable translational inhibitor system

[25,63]

33466

COG3668-ParE

Toxin of plasmid stabilization system

[22,64]

33870

COG4113

PIN domain, present in VapC toxins

[20,59,60]

33875

COG4118-Phd

Antitoxin to translational inhibitor Doc

[65]

33951

COG4226-HicB

HicB of HicAB system (predicted)

[58]

34119

COG4423

Predicted antitoxin of PIN domain toxins (VapC)

[57,60]

34135

COG4456-VagC

Antitoxin of plasmid maintenance system

[66]

34307

COG4691-StbC

Plasmid stability proteins (HigBA family)

[67,68], this study

34891

COG5302-CcdA

Antitoxin of plasmid stabilization system

[27,69]

35058

COG5499

Predicted transcription regulators with HTH domain

[20], this study

41431

pfam01381-Hth_3

Present in antitoxins of HigBA and VapBC families

[20], this study

41452

pfam01402-Hth_4

Present in CopG repressors (RelBE, ParDE, VapBC, and CcdAB families)

[20], this study

41869

pfam01845-CcdB

Toxin of plasmid stabilization system

[69]

41874

pfam01850-PIN

DNA binding PIN domain, present in VapC toxins

[59,60]

42429

pfam02452-PemK

Toxin of the MazEF family

[70]

43931

pfam04014-AbrB

Domain present in MazE and VapB antitoxins

[20], this study

44135

pfam04221-RelB

Antitoxin to translational repressor RelE

[14]

44915

pfam05012-Doc

Toxin of probable translational inhibitor system

[63]

44918

pfam05015-Plasmid_killer

Toxins of the HigBA family

[23], this study

44919

pfam05016-Plasmid_stabil

Toxins of the RelE family

[14], this study

45431

pfam05534-HicB

Member of the HicAB system

[58]

47246

pfam07362-CcdA

Antitoxin of plasmid stabilization system

[27,69]

47831

smart00530-Xre

XRE-like HTH domain present in HigA and VapB

[20], this study

  1. References to 'this study' correspond to domains found in this study upon sequence analysis of described TA candidates. AbrB, AidB regulator; HTH, helix-turn-helix; PIN, homologues of the pilin biogenesis protein pilT amino-terminal domain; XRE, xenobiotic response element.