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Conserved domains on  [gi|489199016|ref|WP_003108276|]
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MULTISPECIES: AbrB/MazE/SpoVT family DNA-binding domain-containing protein [Pseudomonadota]

Protein Classification

AbrB/MazE/SpoVT family DNA-binding domain-containing protein( domain architecture ID 10005093)

AbrB/MazE/SpoVT family DNA-binding domain-containing protein similar to Bacillus subtilis transition state regulatory protein AbrB and Mycobacterium tuberculosis antitoxin VapB27, the antitoxin component of a type II toxin-antitoxin system whose cognate toxin is VapC27

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AbrB COG2002
Bifunctional DNA-binding transcriptional regulator of stationary/sporulation/toxin gene ...
 1-78 6.08e-12

Bifunctional DNA-binding transcriptional regulator of stationary/sporulation/toxin gene expression and antitoxin component of the YhaV-PrlF toxin-antitoxin module [Transcription, Defense mechanisms];


:

Pssm-ID: 441605 [Multi-domain]  Cd Length: 70  Bit Score: 54.98  E-value: 6.08e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489199016  1 MTTLTVTARGQVTFRKDVLQHLGIRPGDKIELDLLPDGrGVLKAARPagTIASFVGLLAGKtqkvaTIEEINEAAAQG 78
Cdd:COG2002   1 MKTVKVTSKGQITIPKEIREALGIKEGDKLEVIVDGDG-IVLKPVKP--PVEELRGLLKGL-----SLEELEEAIREA 70
 
Name Accession Description Interval E-value
AbrB COG2002
Bifunctional DNA-binding transcriptional regulator of stationary/sporulation/toxin gene ...
 1-78 6.08e-12

Bifunctional DNA-binding transcriptional regulator of stationary/sporulation/toxin gene expression and antitoxin component of the YhaV-PrlF toxin-antitoxin module [Transcription, Defense mechanisms];


Pssm-ID: 441605 [Multi-domain]  Cd Length: 70  Bit Score: 54.98  E-value: 6.08e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489199016  1 MTTLTVTARGQVTFRKDVLQHLGIRPGDKIELDLLPDGrGVLKAARPagTIASFVGLLAGKtqkvaTIEEINEAAAQG 78
Cdd:COG2002   1 MKTVKVTSKGQITIPKEIREALGIKEGDKLEVIVDGDG-IVLKPVKP--PVEELRGLLKGL-----SLEELEEAIREA 70
SpoVT_AbrB smart00966
SpoVT / AbrB like domain; This domain is found in AbrB from Bacillus subtilis. The product of ...
 5-48 8.36e-08

SpoVT / AbrB like domain; This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation. AbrB is thought to interact directly with the transcription initiation regions of genes under its control. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator. DNA-binding activity in this AbrB homologue requires hexamerisation. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins.


Pssm-ID: 198034 [Multi-domain]  Cd Length: 45  Bit Score: 44.04  E-value: 8.36e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 489199016    5 TVTARGQVTFRKDVLQHLGIRPGDKIELDLLPDGrGVLKAARPA 48
Cdd:smart00966  2 KVGNSGQVTIPKEVREKLGIKEGDEVELEVDGDG-IILEPVKKA 44
PrlF_antitoxin pfam15937
prlF antitoxin for toxin YhaV_toxin; PrlF_antitoxin is a family of bacterial antitoxins that ...
 5-59 1.54e-05

prlF antitoxin for toxin YhaV_toxin; PrlF_antitoxin is a family of bacterial antitoxins that neutralizes the toxin YhaV. PrlF is labile and forms a homodimer that then binds to the YhaV toxin thereby neutralising its ribonuclease activity. Alone, it can also act as a transcription factor. The YhaV/PrlF complex binds the prlF-yhaV operon, probably regulating its expression negatively. Over-expression of PrlF leads to increased doubling time.


Pssm-ID: 435029  Cd Length: 98  Bit Score: 39.34  E-value: 1.54e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489199016   5 TVTARGQVTFRKDVLQHLGIRPGDKIELDLLPDGRGVL-KAARPAG--TIASFVGLLA 59
Cdd:pfam15937  2 TLTDRGQTTIPATVRKALGLGKRDKIHYTILPDGQVVIsRAAEEADdpVLGAFLGFLA 59
lp_hng_hel_AbrB TIGR01439
looped-hinge helix DNA binding domain, AbrB family; This DNA-binding domain family includes ...
 5-46 3.35e-05

looped-hinge helix DNA binding domain, AbrB family; This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609. [Regulatory functions, DNA interactions]


Pssm-ID: 273625 [Multi-domain]  Cd Length: 43  Bit Score: 37.23  E-value: 3.35e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 489199016   5 TVTARGQVTFRKDVLQHLGIRPGDKIELDLLPDGRGVLKAAR 46
Cdd:TIGR01439  2 TVDKKGQIVIPKEIREKLGLKEGDRLEVIRVEDGEIILRPKR 43
PRK09974 PRK09974
type II toxin-antitoxin system PrlF family antitoxin;
5-59 6.26e-05

type II toxin-antitoxin system PrlF family antitoxin;


Pssm-ID: 236638  Cd Length: 111  Bit Score: 38.11  E-value: 6.26e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489199016   5 TVTARGQVTFRKDVLQHLGIRPGDKIELDLLPDGRGVLKAARPAG---TIASFVGLLA 59
Cdd:PRK09974  13 KLTDRGQTTVPAPVRKALKLKKRDSIHYEILPGGQVFICRLGDEEedpVLGAFLDFLA 70
near_HgcAB NF040962
HgcAB-associated protein; Nearly have the members of this mostly archaeal protein family occur ...
 4-32 4.15e-04

HgcAB-associated protein; Nearly have the members of this mostly archaeal protein family occur in species with methylmercury formation proteins HgcA and HgcB, encoded next to HgcA.


Pssm-ID: 468892  Cd Length: 70  Bit Score: 34.97  E-value: 4.15e-04
                        10        20
                ....*....|....*....|....*....
gi 489199016  4 LTVTARGQVTFRKDVLQHLGIRPGDKIEL 32
Cdd:NF040962  8 VSVDERGQMVLPKEIREKAGIKPGDKLAL 36
 
Name Accession Description Interval E-value
AbrB COG2002
Bifunctional DNA-binding transcriptional regulator of stationary/sporulation/toxin gene ...
 1-78 6.08e-12

Bifunctional DNA-binding transcriptional regulator of stationary/sporulation/toxin gene expression and antitoxin component of the YhaV-PrlF toxin-antitoxin module [Transcription, Defense mechanisms];


Pssm-ID: 441605 [Multi-domain]  Cd Length: 70  Bit Score: 54.98  E-value: 6.08e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489199016  1 MTTLTVTARGQVTFRKDVLQHLGIRPGDKIELDLLPDGrGVLKAARPagTIASFVGLLAGKtqkvaTIEEINEAAAQG 78
Cdd:COG2002   1 MKTVKVTSKGQITIPKEIREALGIKEGDKLEVIVDGDG-IVLKPVKP--PVEELRGLLKGL-----SLEELEEAIREA 70
SpoVT_AbrB smart00966
SpoVT / AbrB like domain; This domain is found in AbrB from Bacillus subtilis. The product of ...
 5-48 8.36e-08

SpoVT / AbrB like domain; This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation. AbrB is thought to interact directly with the transcription initiation regions of genes under its control. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator. DNA-binding activity in this AbrB homologue requires hexamerisation. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins.


Pssm-ID: 198034 [Multi-domain]  Cd Length: 45  Bit Score: 44.04  E-value: 8.36e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 489199016    5 TVTARGQVTFRKDVLQHLGIRPGDKIELDLLPDGrGVLKAARPA 48
Cdd:smart00966  2 KVGNSGQVTIPKEVREKLGIKEGDEVELEVDGDG-IILEPVKKA 44
PrlF_antitoxin pfam15937
prlF antitoxin for toxin YhaV_toxin; PrlF_antitoxin is a family of bacterial antitoxins that ...
 5-59 1.54e-05

prlF antitoxin for toxin YhaV_toxin; PrlF_antitoxin is a family of bacterial antitoxins that neutralizes the toxin YhaV. PrlF is labile and forms a homodimer that then binds to the YhaV toxin thereby neutralising its ribonuclease activity. Alone, it can also act as a transcription factor. The YhaV/PrlF complex binds the prlF-yhaV operon, probably regulating its expression negatively. Over-expression of PrlF leads to increased doubling time.


Pssm-ID: 435029  Cd Length: 98  Bit Score: 39.34  E-value: 1.54e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489199016   5 TVTARGQVTFRKDVLQHLGIRPGDKIELDLLPDGRGVL-KAARPAG--TIASFVGLLA 59
Cdd:pfam15937  2 TLTDRGQTTIPATVRKALGLGKRDKIHYTILPDGQVVIsRAAEEADdpVLGAFLGFLA 59
lp_hng_hel_AbrB TIGR01439
looped-hinge helix DNA binding domain, AbrB family; This DNA-binding domain family includes ...
 5-46 3.35e-05

looped-hinge helix DNA binding domain, AbrB family; This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609. [Regulatory functions, DNA interactions]


Pssm-ID: 273625 [Multi-domain]  Cd Length: 43  Bit Score: 37.23  E-value: 3.35e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 489199016   5 TVTARGQVTFRKDVLQHLGIRPGDKIELDLLPDGRGVLKAAR 46
Cdd:TIGR01439  2 TVDKKGQIVIPKEIREKLGLKEGDRLEVIRVEDGEIILRPKR 43
PRK09974 PRK09974
type II toxin-antitoxin system PrlF family antitoxin;
5-59 6.26e-05

type II toxin-antitoxin system PrlF family antitoxin;


Pssm-ID: 236638  Cd Length: 111  Bit Score: 38.11  E-value: 6.26e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489199016   5 TVTARGQVTFRKDVLQHLGIRPGDKIELDLLPDGRGVLKAARPAG---TIASFVGLLA 59
Cdd:PRK09974  13 KLTDRGQTTVPAPVRKALKLKKRDSIHYEILPGGQVFICRLGDEEedpVLGAFLDFLA 70
near_HgcAB NF040962
HgcAB-associated protein; Nearly have the members of this mostly archaeal protein family occur ...
 4-32 4.15e-04

HgcAB-associated protein; Nearly have the members of this mostly archaeal protein family occur in species with methylmercury formation proteins HgcA and HgcB, encoded next to HgcA.


Pssm-ID: 468892  Cd Length: 70  Bit Score: 34.97  E-value: 4.15e-04
                        10        20
                ....*....|....*....|....*....
gi 489199016  4 LTVTARGQVTFRKDVLQHLGIRPGDKIEL 32
Cdd:NF040962  8 VSVDERGQMVLPKEIREKAGIKPGDKLAL 36
MazE COG2336
Antitoxin component MazE of the MazEF toxin-antitoxin module [Defense mechanisms];
11-70 1.21e-03

Antitoxin component MazE of the MazEF toxin-antitoxin module [Defense mechanisms];


Pssm-ID: 441907  Cd Length: 80  Bit Score: 34.09  E-value: 1.21e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489199016 11 QVTFRKDVLQHLGIRPGDKIELDLLPDGRGVLKAARPAGTIASfvgLLAGKTQKVATIEE 70
Cdd:COG2336  13 GVRIPKALLEQLGLKEGDEVELEVEDGRIVIRPVRRPRYTLEE---LLAGITPENAHEEY 69
 
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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