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Conserved domains on  [gi|497621290|ref|WP_009935474|]
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MULTISPECIES: type II toxin-antitoxin system VapB family antitoxin [Mycobacterium]

Protein Classification

type II toxin-antitoxin system VapB family antitoxin( domain architecture ID 10009307)

type II toxin-antitoxin (TA) system VapB family antitoxin binds to and neutralizes the effect of its cognate VapC toxin; similar to Mycobacterium tuberculosis H37Rv antitoxin VapB15 which neutralizes the effect of its cognate VapC15 toxin

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VapB6 COG5450
Transcription regulator of the Arc/MetJ class [Transcription];
2-63 5.61e-20

Transcription regulator of the Arc/MetJ class [Transcription];


:

Pssm-ID: 444201  Cd Length: 62  Bit Score: 74.54  E-value: 5.61e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 497621290  2 SRTNIDIDDELAAEVMRRFGLTTKRAAVDLALRRLVGSPLSREFLLGLEGVGWEGDLDDLRS 63
Cdd:COG5450   1 MRTNIDLDDDLFAEAVRWTGLKTKKDAVHLALRALLRQRKQKHARVLRGKIGWEGDLDAMRS 62
 
Name Accession Description Interval E-value
VapB6 COG5450
Transcription regulator of the Arc/MetJ class [Transcription];
2-63 5.61e-20

Transcription regulator of the Arc/MetJ class [Transcription];


Pssm-ID: 444201  Cd Length: 62  Bit Score: 74.54  E-value: 5.61e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 497621290  2 SRTNIDIDDELAAEVMRRFGLTTKRAAVDLALRRLVGSPLSREFLLGLEGVGWEGDLDDLRS 63
Cdd:COG5450   1 MRTNIDLDDDLFAEAVRWTGLKTKKDAVHLALRALLRQRKQKHARVLRGKIGWEGDLDAMRS 62
VapB_antitoxin pfam09957
Bacterial antitoxin of type II TA system, VapB; VapB is the antitoxin of a bacterial ...
 2-44 3.06e-15

Bacterial antitoxin of type II TA system, VapB; VapB is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is VapC, pfam05016. The family contains several related antitoxins from Cyanobacteria and Actinobacterial families. Antitoxins of this class carry an N-terminal ribbon-helix-helix domain, RHH, that is highly conserved across all type II bacterial antitoxins, which dimerizes with the RHH domain of a second VapB molecule. A hinge section follows the RHH, with an additional pair of flexible alpha helices at the C-terminus. This C-terminus is the Toxin-binding region of the dimer, and so is specific to the cognate toxin, whereas the RHH domain has the specific function of lying across the RNA-binding groove of the toxin dimer and inactivating the active-site - a more general function of all antitoxins.


Pssm-ID: 462933  Cd Length: 43  Bit Score: 62.26  E-value: 3.06e-15
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 497621290   2 SRTNIDIDDELAAEVMRRFGLTTKRAAVDLALRRLVGSPLSRE 44
Cdd:pfam09957  1 MRTNIEIDDELLAEAIRLTGLKTKRELVNLALRELIQRRKQRE 43
 
Name Accession Description Interval E-value
VapB6 COG5450
Transcription regulator of the Arc/MetJ class [Transcription];
2-63 5.61e-20

Transcription regulator of the Arc/MetJ class [Transcription];


Pssm-ID: 444201  Cd Length: 62  Bit Score: 74.54  E-value: 5.61e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 497621290  2 SRTNIDIDDELAAEVMRRFGLTTKRAAVDLALRRLVGSPLSREFLLGLEGVGWEGDLDDLRS 63
Cdd:COG5450   1 MRTNIDLDDDLFAEAVRWTGLKTKKDAVHLALRALLRQRKQKHARVLRGKIGWEGDLDAMRS 62
VapB_antitoxin pfam09957
Bacterial antitoxin of type II TA system, VapB; VapB is the antitoxin of a bacterial ...
 2-44 3.06e-15

Bacterial antitoxin of type II TA system, VapB; VapB is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is VapC, pfam05016. The family contains several related antitoxins from Cyanobacteria and Actinobacterial families. Antitoxins of this class carry an N-terminal ribbon-helix-helix domain, RHH, that is highly conserved across all type II bacterial antitoxins, which dimerizes with the RHH domain of a second VapB molecule. A hinge section follows the RHH, with an additional pair of flexible alpha helices at the C-terminus. This C-terminus is the Toxin-binding region of the dimer, and so is specific to the cognate toxin, whereas the RHH domain has the specific function of lying across the RNA-binding groove of the toxin dimer and inactivating the active-site - a more general function of all antitoxins.


Pssm-ID: 462933  Cd Length: 43  Bit Score: 62.26  E-value: 3.06e-15
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 497621290   2 SRTNIDIDDELAAEVMRRFGLTTKRAAVDLALRRLVGSPLSRE 44
Cdd:pfam09957  1 MRTNIEIDDELLAEAIRLTGLKTKRELVNLALRELIQRRKQRE 43
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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