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Conserved domains on  [gi|499597540|ref|WP_011278274|]
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AbrB/MazE/SpoVT family DNA-binding domain-containing protein [Sulfolobus acidocaldarius]

Protein Classification

AbrB/MazE/SpoVT family DNA-binding domain-containing protein( domain architecture ID 10659226)

AbrB/MazE/SpoVT family DNA-binding domain-containing protein similar to Sulfolobus solfataricus repressor-like proteins SSo7c3 and Sso7c4

CATH:  2.10.260.10
Gene Ontology:  GO:0003677
SCOP:  4000397

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SpoVT_AbrB smart00966
SpoVT / AbrB like domain; This domain is found in AbrB from Bacillus subtilis. The product of ...
 26-67 6.78e-04

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: 34.79  E-value: 6.78e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 499597540    26 MTIDVRGRIKIPSSFIRELDLKPGEEIYLILTSDKKIVITKD 67
Cdd:smart00966   1 VKVGNSGQVTIPKEVREKLGIKEGDEVELEVDGDGIILEPVK 42
Lipocalin super family cl21528
Lipocalin / cytosolic fatty-acid binding protein family; Lipocalins are transporters for small ...
 38-116 4.07e-03

Lipocalin / cytosolic fatty-acid binding protein family; Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel.


The actual alignment was detected with superfamily member PLN02372:

Pssm-ID: 473899 [Multi-domain]  Cd Length: 455  Bit Score: 35.59  E-value: 4.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499597540  38 SSFIRElDLKPGEEIYLILTSDKKI-----VITKDGLPQNSELEERVKELEE------KYERLAKELGRLEFDFARYLRR 106
Cdd:PLN02372 347 SDFVRT-DNTCGPEPPLLERLEKDVeegekTIVKEARQIEEELEKEVEKLGKeeeslfKRVALEEGLKELEQDEENFLKE 425

                         90
                 ....*....|
gi 499597540 107 LSKDETKYQQ 116
Cdd:PLN02372 426 LSKEEKELLE 435
 
Name Accession Description Interval E-value
SpoVT_AbrB smart00966
SpoVT / AbrB like domain; This domain is found in AbrB from Bacillus subtilis. The product of ...
 26-67 6.78e-04

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: 34.79  E-value: 6.78e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 499597540    26 MTIDVRGRIKIPSSFIRELDLKPGEEIYLILTSDKKIVITKD 67
Cdd:smart00966   1 VKVGNSGQVTIPKEVREKLGIKEGDEVELEVDGDGIILEPVK 42
MazE COG2336
Antitoxin component MazE of the MazEF toxin-antitoxin module [Defense mechanisms];
34-95 4.06e-03

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


Pssm-ID: 441907  Cd Length: 80  Bit Score: 33.71  E-value: 4.06e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499597540  34 IKIPSSFIRELDLKPGEEIYLILTsDKKIVITKDGLPQNSeLEERVKELEEKY----ERLAKELGR 95
Cdd:COG2336   14 VRIPKALLEQLGLKEGDEVELEVE-DGRIVIRPVRRPRYT-LEELLAGITPENaheeYDWGKPVGK 77
PLN02372 PLN02372
violaxanthin de-epoxidase
 38-116 4.07e-03

violaxanthin de-epoxidase


Pssm-ID: 215212 [Multi-domain]  Cd Length: 455  Bit Score: 35.59  E-value: 4.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499597540  38 SSFIRElDLKPGEEIYLILTSDKKI-----VITKDGLPQNSELEERVKELEE------KYERLAKELGRLEFDFARYLRR 106
Cdd:PLN02372 347 SDFVRT-DNTCGPEPPLLERLEKDVeegekTIVKEARQIEEELEKEVEKLGKeeeslfKRVALEEGLKELEQDEENFLKE 425

                         90
                 ....*....|
gi 499597540 107 LSKDETKYQQ 116
Cdd:PLN02372 426 LSKEEKELLE 435
lp_hng_hel_AbrB TIGR01439
looped-hinge helix DNA binding domain, AbrB family; This DNA-binding domain family includes ...
 27-64 4.10e-03

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: 33.00  E-value: 4.10e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 499597540   27 TIDVRGRIKIPSSFIRELDLKPGEEIYLILTSDKKIVI 64
Cdd:TIGR01439   2 TVDKKGQIVIPKEIREKLGLKEGDRLEVIRVEDGEIIL 39
 
Name Accession Description Interval E-value
SpoVT_AbrB smart00966
SpoVT / AbrB like domain; This domain is found in AbrB from Bacillus subtilis. The product of ...
 26-67 6.78e-04

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: 34.79  E-value: 6.78e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 499597540    26 MTIDVRGRIKIPSSFIRELDLKPGEEIYLILTSDKKIVITKD 67
Cdd:smart00966   1 VKVGNSGQVTIPKEVREKLGIKEGDEVELEVDGDGIILEPVK 42
MazE COG2336
Antitoxin component MazE of the MazEF toxin-antitoxin module [Defense mechanisms];
34-95 4.06e-03

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


Pssm-ID: 441907  Cd Length: 80  Bit Score: 33.71  E-value: 4.06e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499597540  34 IKIPSSFIRELDLKPGEEIYLILTsDKKIVITKDGLPQNSeLEERVKELEEKY----ERLAKELGR 95
Cdd:COG2336   14 VRIPKALLEQLGLKEGDEVELEVE-DGRIVIRPVRRPRYT-LEELLAGITPENaheeYDWGKPVGK 77
PLN02372 PLN02372
violaxanthin de-epoxidase
 38-116 4.07e-03

violaxanthin de-epoxidase


Pssm-ID: 215212 [Multi-domain]  Cd Length: 455  Bit Score: 35.59  E-value: 4.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499597540  38 SSFIRElDLKPGEEIYLILTSDKKI-----VITKDGLPQNSELEERVKELEE------KYERLAKELGRLEFDFARYLRR 106
Cdd:PLN02372 347 SDFVRT-DNTCGPEPPLLERLEKDVeegekTIVKEARQIEEELEKEVEKLGKeeeslfKRVALEEGLKELEQDEENFLKE 425

                         90
                 ....*....|
gi 499597540 107 LSKDETKYQQ 116
Cdd:PLN02372 426 LSKEEKELLE 435
lp_hng_hel_AbrB TIGR01439
looped-hinge helix DNA binding domain, AbrB family; This DNA-binding domain family includes ...
 27-64 4.10e-03

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: 33.00  E-value: 4.10e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 499597540   27 TIDVRGRIKIPSSFIRELDLKPGEEIYLILTSDKKIVI 64
Cdd:TIGR01439   2 TVDKKGQIVIPKEIREKLGLKEGDRLEVIRVEDGEIIL 39
 
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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