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Conserved domains on  [gi|446284367|ref|WP_000362222|]
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MULTISPECIES: DnaD domain-containing protein [Staphylococcus]

Protein Classification

DnaD domain-containing protein( domain architecture ID 11467629)

DnaD domain-containing protein which may be a primosomeal protein in Bacillus subtilis which participates in replication fork restart or a phage-associated protein also found in bacilli and clostridia

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DnaD COG3935
DNA replication protein DnaD [Replication, recombination and repair];
125-223 2.24e-28

DNA replication protein DnaD [Replication, recombination and repair];


:

Pssm-ID: 443136  Cd Length: 103  Bit Score: 103.17  E-value: 2.24e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446284367 125 LFRVLEDTFARPLSPYEIETLNQWIDVDKHDTAIIQAALDEANSLNKLSFKYMDRILLNWKKNNVKTIDDSRKIREKFNK 204
Cdd:COG3935    1 LFEFYEQNFGRPLSPFEIEKINKWLDEDGFSPELILEALKEAVENGKRNFKYIDRILKNWKKKGIKTVEDAEAYEKKFKK 80

                         90       100
                 ....*....|....*....|...
gi 446284367 205 PKMTHTVKTVP----KFDWLNGE 223
Cdd:COG3935   81 RKKKKTSKSKSnfeqKPDWYDKE 103
 
Name Accession Description Interval E-value
DnaD COG3935
DNA replication protein DnaD [Replication, recombination and repair];
125-223 2.24e-28

DNA replication protein DnaD [Replication, recombination and repair];


Pssm-ID: 443136  Cd Length: 103  Bit Score: 103.17  E-value: 2.24e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446284367 125 LFRVLEDTFARPLSPYEIETLNQWIDVDKHDTAIIQAALDEANSLNKLSFKYMDRILLNWKKNNVKTIDDSRKIREKFNK 204
Cdd:COG3935    1 LFEFYEQNFGRPLSPFEIEKINKWLDEDGFSPELILEALKEAVENGKRNFKYIDRILKNWKKKGIKTVEDAEAYEKKFKK 80

                         90       100
                 ....*....|....*....|...
gi 446284367 205 PKMTHTVKTVP----KFDWLNGE 223
Cdd:COG3935   81 RKKKKTSKSKSnfeqKPDWYDKE 103
DnaD_dom TIGR01446
DnaD and phage-associated domain; This model represents the conserved domain of DnaD, part of ...
 125-197 1.40e-19

DnaD and phage-associated domain; This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Prophage functions]


Pssm-ID: 273630  Cd Length: 73  Bit Score: 79.27  E-value: 1.40e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446284367  125 LFRVLEDTFARPLSPYEIETLNQWIDVDKHDTAIIQAALDEANSLNKLSFKYMDRILLNWKKNNVKTIDDSRK 197
Cdd:TIGR01446   1 LYDFFEENFGRMLSPFEMEDLKYWLDEFGNDPELVKEALKEAVSNNKANYKYIDAILNNWKNNGIKTVEDVEA 73
DnaB_2 pfam07261
Replication initiation and membrane attachment; This family consists of several bacterial ...
 128-197 6.83e-19

Replication initiation and membrane attachment; This family consists of several bacterial replication initiation and membrane attachment (DnaB) proteins, as well as DnaD which is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication. DnaD has been merged into this family. This family also includes Ftn6, a cyanobacterial-specific divisome component possibly playing a role at the interface between DNA replication and cell division. Ftn6 possesses a conserved domain localized within the N-terminus of the proteins. This domain, named FND, exhibits sequence and structure similarities with the DnaD-like domains pfam04271 now merged into pfam07261.


Pssm-ID: 462127  Cd Length: 70  Bit Score: 77.58  E-value: 6.83e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446284367  128 VLEDTFARPLSPYEIETLNQWIDVDKHDTAIIQAALDEANSLNKLSFKYMDRILLNWKKNNVKTIDDSRK 197
Cdd:pfam07261   1 FIEQEFGRPLSPSEIETILYWLDDLGLSPELILEALEYAVSKGKRNFRYIEKILRNWAEKGIKTVEQAEE 70
 
Name Accession Description Interval E-value
DnaD COG3935
DNA replication protein DnaD [Replication, recombination and repair];
125-223 2.24e-28

DNA replication protein DnaD [Replication, recombination and repair];


Pssm-ID: 443136  Cd Length: 103  Bit Score: 103.17  E-value: 2.24e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446284367 125 LFRVLEDTFARPLSPYEIETLNQWIDVDKHDTAIIQAALDEANSLNKLSFKYMDRILLNWKKNNVKTIDDSRKIREKFNK 204
Cdd:COG3935    1 LFEFYEQNFGRPLSPFEIEKINKWLDEDGFSPELILEALKEAVENGKRNFKYIDRILKNWKKKGIKTVEDAEAYEKKFKK 80

                         90       100
                 ....*....|....*....|...
gi 446284367 205 PKMTHTVKTVP----KFDWLNGE 223
Cdd:COG3935   81 RKKKKTSKSKSnfeqKPDWYDKE 103
DnaD_dom TIGR01446
DnaD and phage-associated domain; This model represents the conserved domain of DnaD, part of ...
 125-197 1.40e-19

DnaD and phage-associated domain; This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Prophage functions]


Pssm-ID: 273630  Cd Length: 73  Bit Score: 79.27  E-value: 1.40e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446284367  125 LFRVLEDTFARPLSPYEIETLNQWIDVDKHDTAIIQAALDEANSLNKLSFKYMDRILLNWKKNNVKTIDDSRK 197
Cdd:TIGR01446   1 LYDFFEENFGRMLSPFEMEDLKYWLDEFGNDPELVKEALKEAVSNNKANYKYIDAILNNWKNNGIKTVEDVEA 73
DnaB_2 pfam07261
Replication initiation and membrane attachment; This family consists of several bacterial ...
 128-197 6.83e-19

Replication initiation and membrane attachment; This family consists of several bacterial replication initiation and membrane attachment (DnaB) proteins, as well as DnaD which is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication. DnaD has been merged into this family. This family also includes Ftn6, a cyanobacterial-specific divisome component possibly playing a role at the interface between DNA replication and cell division. Ftn6 possesses a conserved domain localized within the N-terminus of the proteins. This domain, named FND, exhibits sequence and structure similarities with the DnaD-like domains pfam04271 now merged into pfam07261.


Pssm-ID: 462127  Cd Length: 70  Bit Score: 77.58  E-value: 6.83e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446284367  128 VLEDTFARPLSPYEIETLNQWIDVDKHDTAIIQAALDEANSLNKLSFKYMDRILLNWKKNNVKTIDDSRK 197
Cdd:pfam07261   1 FIEQEFGRPLSPSEIETILYWLDDLGLSPELILEALEYAVSKGKRNFRYIEKILRNWAEKGIKTVEQAEE 70
 
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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