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Conserved domains on  [gi|446651203|ref|WP_000728549|]
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MULTISPECIES: DNA replication protein DnaD [Bacillus]

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];
129-232 6.50e-35

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


:

Pssm-ID: 443136  Cd Length: 103  Bit Score: 120.12  E-value: 6.50e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446651203 129 LYTVFEKEFGRPLSPFECETLGMWEDQDQHHPNLIQAALREAVMSGKLNFRYIDRILFEWKKNGIKTVDQAQNQGRKFRA 208
Cdd:COG3935    1 LFEFYEQNFGRPLSPFEIEKINKWLDEDGFSPELILEALKEAVENGKRNFKYIDRILKNWKKKGIKTVEDAEAYEKKFKK 80

                         90       100
                 ....*....|....*....|....
gi 446651203 209 NqqRTQQTTKQETKFTGKVPFYNW 232
Cdd:COG3935   81 R--KKKKTSKSKSNFEQKPDWYDK 102
DnaD_Mollicutes super family cl37469
DnaD family protein, Mollicutes type; This model describes the full length of a family of ...
 10-149 3.88e-12

DnaD family protein, Mollicutes type; This model describes the full length of a family of proteins in the Mollicutes (Mycoplasma, Spiroplasma, Mesoplasma, etc.) homologous to the N-terminal region of DnaD from Bacillus subtilis. [DNA metabolism, DNA replication, recombination, and repair]


The actual alignment was detected with superfamily member TIGR04548:

Pssm-ID: 275341  Cd Length: 178  Bit Score: 62.74  E-value: 3.88e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446651203   10 FEQGSIAIPKLLMMHYKKLGLNETEFMVVLHVHTFLESGNSFPTPSEISERMTITEMKCMEVIQTLIQKGFLSLEGgqks 89
Cdd:TIGR04548   4 LKKGLISKKKLLLENYKKIGLTENQVMIILMIMHLSDDDKKFITPNELAKYMNLSESEIEKEIEKLVEKDLIKIKP---- 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446651203   90 eammcESYSLQPLWEKILHFLMNESIEEEQKEikqlqvnLYTVFEKEFGRPLSPFECETL 149
Cdd:TIGR04548  80 -----KEIDFSPLFNKIAIIIENEYLNKENKD-------FFQQIEEKLGFKLTEDQKAEL 127
 
Name Accession Description Interval E-value
DnaD COG3935
DNA replication protein DnaD [Replication, recombination and repair];
129-232 6.50e-35

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


Pssm-ID: 443136  Cd Length: 103  Bit Score: 120.12  E-value: 6.50e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446651203 129 LYTVFEKEFGRPLSPFECETLGMWEDQDQHHPNLIQAALREAVMSGKLNFRYIDRILFEWKKNGIKTVDQAQNQGRKFRA 208
Cdd:COG3935    1 LFEFYEQNFGRPLSPFEIEKINKWLDEDGFSPELILEALKEAVENGKRNFKYIDRILKNWKKKGIKTVEDAEAYEKKFKK 80

                         90       100
                 ....*....|....*....|....
gi 446651203 209 NqqRTQQTTKQETKFTGKVPFYNW 232
Cdd:COG3935   81 R--KKKKTSKSKSNFEQKPDWYDK 102
DnaB_2 pfam07261
Replication initiation and membrane attachment; This family consists of several bacterial ...
 132-201 1.22e-25

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: 95.29  E-value: 1.22e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446651203  132 VFEKEFGRPLSPFECETLGMWEDQDQHHPNLIQAALREAVMSGKLNFRYIDRILFEWKKNGIKTVDQAQN 201
Cdd:pfam07261   1 FIEQEFGRPLSPSEIETILYWLDDLGLSPELILEALEYAVSKGKRNFRYIEKILRNWAEKGIKTVEQAEE 70
DnaD_dom TIGR01446
DnaD and phage-associated domain; This model represents the conserved domain of DnaD, part of ...
 129-201 3.73e-25

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: 93.90  E-value: 3.73e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446651203  129 LYTVFEKEFGRPLSPFECETLGMWEDQDQHHPNLIQAALREAVMSGKLNFRYIDRILFEWKKNGIKTVDQAQN 201
Cdd:TIGR01446   1 LYDFFEENFGRMLSPFEMEDLKYWLDEFGNDPELVKEALKEAVSNNKANYKYIDAILNNWKNNGIKTVEDVEA 73
DnaD_Mollicutes TIGR04548
DnaD family protein, Mollicutes type; This model describes the full length of a family of ...
 10-149 3.88e-12

DnaD family protein, Mollicutes type; This model describes the full length of a family of proteins in the Mollicutes (Mycoplasma, Spiroplasma, Mesoplasma, etc.) homologous to the N-terminal region of DnaD from Bacillus subtilis. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 275341  Cd Length: 178  Bit Score: 62.74  E-value: 3.88e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446651203   10 FEQGSIAIPKLLMMHYKKLGLNETEFMVVLHVHTFLESGNSFPTPSEISERMTITEMKCMEVIQTLIQKGFLSLEGgqks 89
Cdd:TIGR04548   4 LKKGLISKKKLLLENYKKIGLTENQVMIILMIMHLSDDDKKFITPNELAKYMNLSESEIEKEIEKLVEKDLIKIKP---- 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446651203   90 eammcESYSLQPLWEKILHFLMNESIEEEQKEikqlqvnLYTVFEKEFGRPLSPFECETL 149
Cdd:TIGR04548  80 -----KEIDFSPLFNKIAIIIENEYLNKENKD-------FFQQIEEKLGFKLTEDQKAEL 127
TrmB pfam01978
Sugar-specific transcriptional regulator TrmB; One member of this family, TrmB, has been shown ...
 26-80 3.97e-04

Sugar-specific transcriptional regulator TrmB; One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.


Pssm-ID: 396525 [Multi-domain]  Cd Length: 67  Bit Score: 37.89  E-value: 3.97e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446651203   26 KKLGLNETEFMVVLhvhTFLESGNSfpTPSEISERMTITEMKCMEVIQTLIQKGF 80
Cdd:pfam01978   2 QKLGLSEYEAKVYL---ALLKLGPA--TADEIAEESGVPRSKVYEVLRSLEDKGL 51
 
Name Accession Description Interval E-value
DnaD COG3935
DNA replication protein DnaD [Replication, recombination and repair];
129-232 6.50e-35

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


Pssm-ID: 443136  Cd Length: 103  Bit Score: 120.12  E-value: 6.50e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446651203 129 LYTVFEKEFGRPLSPFECETLGMWEDQDQHHPNLIQAALREAVMSGKLNFRYIDRILFEWKKNGIKTVDQAQNQGRKFRA 208
Cdd:COG3935    1 LFEFYEQNFGRPLSPFEIEKINKWLDEDGFSPELILEALKEAVENGKRNFKYIDRILKNWKKKGIKTVEDAEAYEKKFKK 80

                         90       100
                 ....*....|....*....|....
gi 446651203 209 NqqRTQQTTKQETKFTGKVPFYNW 232
Cdd:COG3935   81 R--KKKKTSKSKSNFEQKPDWYDK 102
DnaB_2 pfam07261
Replication initiation and membrane attachment; This family consists of several bacterial ...
 132-201 1.22e-25

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: 95.29  E-value: 1.22e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446651203  132 VFEKEFGRPLSPFECETLGMWEDQDQHHPNLIQAALREAVMSGKLNFRYIDRILFEWKKNGIKTVDQAQN 201
Cdd:pfam07261   1 FIEQEFGRPLSPSEIETILYWLDDLGLSPELILEALEYAVSKGKRNFRYIEKILRNWAEKGIKTVEQAEE 70
DnaD_dom TIGR01446
DnaD and phage-associated domain; This model represents the conserved domain of DnaD, part of ...
 129-201 3.73e-25

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: 93.90  E-value: 3.73e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446651203  129 LYTVFEKEFGRPLSPFECETLGMWEDQDQHHPNLIQAALREAVMSGKLNFRYIDRILFEWKKNGIKTVDQAQN 201
Cdd:TIGR01446   1 LYDFFEENFGRMLSPFEMEDLKYWLDEFGNDPELVKEALKEAVSNNKANYKYIDAILNNWKNNGIKTVEDVEA 73
DnaD_Mollicutes TIGR04548
DnaD family protein, Mollicutes type; This model describes the full length of a family of ...
 10-149 3.88e-12

DnaD family protein, Mollicutes type; This model describes the full length of a family of proteins in the Mollicutes (Mycoplasma, Spiroplasma, Mesoplasma, etc.) homologous to the N-terminal region of DnaD from Bacillus subtilis. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 275341  Cd Length: 178  Bit Score: 62.74  E-value: 3.88e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446651203   10 FEQGSIAIPKLLMMHYKKLGLNETEFMVVLHVHTFLESGNSFPTPSEISERMTITEMKCMEVIQTLIQKGFLSLEGgqks 89
Cdd:TIGR04548   4 LKKGLISKKKLLLENYKKIGLTENQVMIILMIMHLSDDDKKFITPNELAKYMNLSESEIEKEIEKLVEKDLIKIKP---- 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446651203   90 eammcESYSLQPLWEKILHFLMNESIEEEQKEikqlqvnLYTVFEKEFGRPLSPFECETL 149
Cdd:TIGR04548  80 -----KEIDFSPLFNKIAIIIENEYLNKENKD-------FFQQIEEKLGFKLTEDQKAEL 127
TrmB pfam01978
Sugar-specific transcriptional regulator TrmB; One member of this family, TrmB, has been shown ...
 26-80 3.97e-04

Sugar-specific transcriptional regulator TrmB; One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.


Pssm-ID: 396525 [Multi-domain]  Cd Length: 67  Bit Score: 37.89  E-value: 3.97e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446651203   26 KKLGLNETEFMVVLhvhTFLESGNSfpTPSEISERMTITEMKCMEVIQTLIQKGF 80
Cdd:pfam01978   2 QKLGLSEYEAKVYL---ALLKLGPA--TADEIAEESGVPRSKVYEVLRSLEDKGL 51
 
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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