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Conserved domains on  [gi|295789575]
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Chain U, Protein sopB

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK13698 super family cl32924
ParB/RepB/Spo0J family plasmid partition protein;
1-121 2.66e-75

ParB/RepB/Spo0J family plasmid partition protein;


The actual alignment was detected with superfamily member PRK13698:

Pssm-ID: 184254 [Multi-domain]  Cd Length: 323  Bit Score: 225.88  E-value: 2.66e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295789575   1 GSHYRPTSAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGDALQKAFTDK 80
Cdd:PRK13698 152 GNDYRPTSAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFAHPGELSARSGEALQKAFTDK 231

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 295789575  81 EELLKQQASNLHEQKKAGVIFEADEVITLLTSVLKTSSASR 121
Cdd:PRK13698 232 EELLKQQTSNLHEQKKAGVIFETEEVITLLTSVLKTSSASR 272
 
Name Accession Description Interval E-value
PRK13698 PRK13698
ParB/RepB/Spo0J family plasmid partition protein;
1-121 2.66e-75

ParB/RepB/Spo0J family plasmid partition protein;


Pssm-ID: 184254 [Multi-domain]  Cd Length: 323  Bit Score: 225.88  E-value: 2.66e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295789575   1 GSHYRPTSAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGDALQKAFTDK 80
Cdd:PRK13698 152 GNDYRPTSAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFAHPGELSARSGEALQKAFTDK 231

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 295789575  81 EELLKQQASNLHEQKKAGVIFEADEVITLLTSVLKTSSASR 121
Cdd:PRK13698 232 EELLKQQTSNLHEQKKAGVIFETEEVITLLTSVLKTSSASR 272
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 6-92 1.00e-22

ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.


Pssm-ID: 272946 [Multi-domain]  Cd Length: 187  Bit Score: 87.43  E-value: 1.00e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295789575    6 PTSAYERGQRYASRLQnEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGDALQKAFTDKEELLK 85
Cdd:TIGR00180 102 DLSPIEEAQAYKRLLE-KFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASGLLSSGHARLLLALKKKPKLQE 180


                  ....*..
gi 295789575   86 QQASNLH 92
Cdd:TIGR00180 181 LLASIII 187
SoPB_HTH pfam18090
Centromere-binding protein HTH domain; This domain is found in centromere-binding protein ...
 8-80 7.09e-07

Centromere-binding protein HTH domain; This domain is found in centromere-binding protein (SopB). SopB displays an intriguing range of DNA-binding properties essential for partition; it binds the centromere to form a partition complex, which recruits NTPase (SopA), and it also inhibits SopA polymerization. The domain has a helix-turn-helix (HTH) structure and is thought to be the specific DNA-binding domain mainly through residues from the recognition helix, alpha 3, of the HTH. The domain has show structural similarity to the DNA-binding domains of P1 ParB and KorB.


Pssm-ID: 375543  Cd Length: 75  Bit Score: 43.56  E-value: 7.09e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 295789575    8 SAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGDALQKAFTDK 80
Cdd:pfam18090   2 SAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGDALQKAFTDK 74
 
Name Accession Description Interval E-value
PRK13698 PRK13698
ParB/RepB/Spo0J family plasmid partition protein;
1-121 2.66e-75

ParB/RepB/Spo0J family plasmid partition protein;


Pssm-ID: 184254 [Multi-domain]  Cd Length: 323  Bit Score: 225.88  E-value: 2.66e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295789575   1 GSHYRPTSAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGDALQKAFTDK 80
Cdd:PRK13698 152 GNDYRPTSAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFAHPGELSARSGEALQKAFTDK 231

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 295789575  81 EELLKQQASNLHEQKKAGVIFEADEVITLLTSVLKTSSASR 121
Cdd:PRK13698 232 EELLKQQTSNLHEQKKAGVIFETEEVITLLTSVLKTSSASR 272
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 6-92 1.00e-22

ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.


Pssm-ID: 272946 [Multi-domain]  Cd Length: 187  Bit Score: 87.43  E-value: 1.00e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295789575    6 PTSAYERGQRYASRLQnEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGDALQKAFTDKEELLK 85
Cdd:TIGR00180 102 DLSPIEEAQAYKRLLE-KFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAIPEASGLLSSGHARLLLALKKKPKLQE 180


                  ....*..
gi 295789575   86 QQASNLH 92
Cdd:TIGR00180 181 LLASIII 187
SoPB_HTH pfam18090
Centromere-binding protein HTH domain; This domain is found in centromere-binding protein ...
 8-80 7.09e-07

Centromere-binding protein HTH domain; This domain is found in centromere-binding protein (SopB). SopB displays an intriguing range of DNA-binding properties essential for partition; it binds the centromere to form a partition complex, which recruits NTPase (SopA), and it also inhibits SopA polymerization. The domain has a helix-turn-helix (HTH) structure and is thought to be the specific DNA-binding domain mainly through residues from the recognition helix, alpha 3, of the HTH. The domain has show structural similarity to the DNA-binding domains of P1 ParB and KorB.


Pssm-ID: 375543  Cd Length: 75  Bit Score: 43.56  E-value: 7.09e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 295789575    8 SAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGDALQKAFTDK 80
Cdd:pfam18090   2 SAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGDALQKAFTDK 74
 
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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