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Conserved domains on  [gi|1070099596|ref|YP_009283208|]
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replisome organizer [Lactococcus phage 50101]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Phage_rep_org_N super family cl09889
N-terminal phage replisome organizer (Phage_rep_org_N); This entry represents the N-terminal ...
 1-115 2.77e-33

N-terminal phage replisome organizer (Phage_rep_org_N); This entry represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region is N-terminal to the low-complexity region.


The actual alignment was detected with superfamily member TIGR01714:

Pssm-ID: 447848  Cd Length: 119  Bit Score: 118.36  E-value: 2.77e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070099596   1 MRLKENFFDSDEMIILENMDNGDgiIYSNILLKLYLRSLKYEGRLMFNERIPFNPQMLSTIVRHPVGVVEKALKAFVDLG 80
Cdd:TIGR01714   2 IKLKVNFFDSKEIKLLEKMPEGD--THTIIWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLESLG 79

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1070099596  81 LVEVMDNGAIYMLDIQNFIGKTTTEADRIKAYRSK 115
Cdd:TIGR01714  80 LIEKKNNGDIFLENWEKHVGSDSASARRERKFRRN 114
DnaD COG3935
DNA replication protein DnaD [Replication, recombination and repair];
170-270 8.50e-16

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


:

Pssm-ID: 443136  Cd Length: 103  Bit Score: 71.59  E-value: 8.50e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070099596 170 LIELYQTNFG-IVKPILYDDLKA--DLKDYGLELIIEAVKRAVKRQ-REYAYAQGILKSWNRSGIKTLEQAKAEEVSFQN 245
Cdd:COG3935     1 LFEFYEQNFGrPLSPFEIEKINKwlDEDGFSPELILEALKEAVENGkRNFKYIDRILKNWKKKGIKTVEDAEAYEKKFKK 80

                          90       100
                  ....*....|....*....|....*
gi 1070099596 246 KsqNNQNKFQQQKPVKKAPDWSNQR 270
Cdd:COG3935    81 R--KKKKTSKSKSNFEQKPDWYDKE 103
 
Name Accession Description Interval E-value
phage_rep_org_N TIGR01714
phage replisome organizer, putative, N-terminal region; This model represents the N-terminal ...
 1-115 2.77e-33

phage replisome organizer, putative, N-terminal region; This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region. [Mobile and extrachromosomal element functions, Prophage functions]


Pssm-ID: 130775  Cd Length: 119  Bit Score: 118.36  E-value: 2.77e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070099596   1 MRLKENFFDSDEMIILENMDNGDgiIYSNILLKLYLRSLKYEGRLMFNERIPFNPQMLSTIVRHPVGVVEKALKAFVDLG 80
Cdd:TIGR01714   2 IKLKVNFFDSKEIKLLEKMPEGD--THTIIWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLESLG 79

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1070099596  81 LVEVMDNGAIYMLDIQNFIGKTTTEADRIKAYRSK 115
Cdd:TIGR01714  80 LIEKKNNGDIFLENWEKHVGSDSASARRERKFRRN 114
Phage_rep_org_N pfam09681
N-terminal phage replisome organizer (Phage_rep_org_N); This entry represents the N-terminal ...
 1-115 4.37e-32

N-terminal phage replisome organizer (Phage_rep_org_N); This entry represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region is N-terminal to the low-complexity region.


Pssm-ID: 430749  Cd Length: 121  Bit Score: 115.18  E-value: 4.37e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070099596   1 MRLKENFFDSDEMIILENMDNGDgiIYSNILLKLYLRSLKYE--GRLMFNERIPFNPQMLSTIVRHPVGVVEKALKAFVD 78
Cdd:pfam09681   2 IKLKVNMFDDEKIKLIEKMPEGD--TYIVIWLKLLLLSGKTNnnGYIMLSENIPYTAEMLATIFNRPLNTVRLALQTFKQ 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1070099596  79 LGLVEVMDNGAIYMLDIQNFIGKTTTEADRIKAYRSK 115
Cdd:pfam09681  80 FGMIEISDNGAIKITNWSKHQNLESLEKHRERTRRRK 116
DnaD COG3935
DNA replication protein DnaD [Replication, recombination and repair];
170-270 8.50e-16

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


Pssm-ID: 443136  Cd Length: 103  Bit Score: 71.59  E-value: 8.50e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070099596 170 LIELYQTNFG-IVKPILYDDLKA--DLKDYGLELIIEAVKRAVKRQ-REYAYAQGILKSWNRSGIKTLEQAKAEEVSFQN 245
Cdd:COG3935     1 LFEFYEQNFGrPLSPFEIEKINKwlDEDGFSPELILEALKEAVENGkRNFKYIDRILKNWKKKGIKTVEDAEAYEKKFKK 80

                          90       100
                  ....*....|....*....|....*
gi 1070099596 246 KsqNNQNKFQQQKPVKKAPDWSNQR 270
Cdd:COG3935    81 R--KKKKTSKSKSNFEQKPDWYDKE 103
DnaD_dom TIGR01446
DnaD and phage-associated domain; This model represents the conserved domain of DnaD, part of ...
 170-238 8.54e-12

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: 59.62  E-value: 8.54e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1070099596 170 LIELYQTNFGIVK-PILYDDLKADLKDYG--LELIIEAVKRAVKRQ-REYAYAQGILKSWNRSGIKTLEQAKA 238
Cdd:TIGR01446   1 LYDFFEENFGRMLsPFEMEDLKYWLDEFGndPELVKEALKEAVSNNkANYKYIDAILNNWKNNGIKTVEDVEA 73
DnaB_2 pfam07261
Replication initiation and membrane attachment; This family consists of several bacterial ...
 173-238 6.99e-10

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: 54.08  E-value: 6.99e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070099596 173 LYQTNFG-IVKPILYDDLKADLKDYGL--ELIIEAVKRAVKRQ-REYAYAQGILKSWNRSGIKTLEQAKA 238
Cdd:pfam07261   1 FIEQEFGrPLSPSEIETILYWLDDLGLspELILEALEYAVSKGkRNFRYIEKILRNWAEKGIKTVEQAEE 70
 
Name Accession Description Interval E-value
phage_rep_org_N TIGR01714
phage replisome organizer, putative, N-terminal region; This model represents the N-terminal ...
 1-115 2.77e-33

phage replisome organizer, putative, N-terminal region; This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region. [Mobile and extrachromosomal element functions, Prophage functions]


Pssm-ID: 130775  Cd Length: 119  Bit Score: 118.36  E-value: 2.77e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070099596   1 MRLKENFFDSDEMIILENMDNGDgiIYSNILLKLYLRSLKYEGRLMFNERIPFNPQMLSTIVRHPVGVVEKALKAFVDLG 80
Cdd:TIGR01714   2 IKLKVNFFDSKEIKLLEKMPEGD--THTIIWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLESLG 79

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1070099596  81 LVEVMDNGAIYMLDIQNFIGKTTTEADRIKAYRSK 115
Cdd:TIGR01714  80 LIEKKNNGDIFLENWEKHVGSDSASARRERKFRRN 114
Phage_rep_org_N pfam09681
N-terminal phage replisome organizer (Phage_rep_org_N); This entry represents the N-terminal ...
 1-115 4.37e-32

N-terminal phage replisome organizer (Phage_rep_org_N); This entry represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region is N-terminal to the low-complexity region.


Pssm-ID: 430749  Cd Length: 121  Bit Score: 115.18  E-value: 4.37e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070099596   1 MRLKENFFDSDEMIILENMDNGDgiIYSNILLKLYLRSLKYE--GRLMFNERIPFNPQMLSTIVRHPVGVVEKALKAFVD 78
Cdd:pfam09681   2 IKLKVNMFDDEKIKLIEKMPEGD--TYIVIWLKLLLLSGKTNnnGYIMLSENIPYTAEMLATIFNRPLNTVRLALQTFKQ 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1070099596  79 LGLVEVMDNGAIYMLDIQNFIGKTTTEADRIKAYRSK 115
Cdd:pfam09681  80 FGMIEISDNGAIKITNWSKHQNLESLEKHRERTRRRK 116
DnaD COG3935
DNA replication protein DnaD [Replication, recombination and repair];
170-270 8.50e-16

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


Pssm-ID: 443136  Cd Length: 103  Bit Score: 71.59  E-value: 8.50e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070099596 170 LIELYQTNFG-IVKPILYDDLKA--DLKDYGLELIIEAVKRAVKRQ-REYAYAQGILKSWNRSGIKTLEQAKAEEVSFQN 245
Cdd:COG3935     1 LFEFYEQNFGrPLSPFEIEKINKwlDEDGFSPELILEALKEAVENGkRNFKYIDRILKNWKKKGIKTVEDAEAYEKKFKK 80

                          90       100
                  ....*....|....*....|....*
gi 1070099596 246 KsqNNQNKFQQQKPVKKAPDWSNQR 270
Cdd:COG3935    81 R--KKKKTSKSKSNFEQKPDWYDKE 103
DnaD_dom TIGR01446
DnaD and phage-associated domain; This model represents the conserved domain of DnaD, part of ...
 170-238 8.54e-12

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: 59.62  E-value: 8.54e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1070099596 170 LIELYQTNFGIVK-PILYDDLKADLKDYG--LELIIEAVKRAVKRQ-REYAYAQGILKSWNRSGIKTLEQAKA 238
Cdd:TIGR01446   1 LYDFFEENFGRMLsPFEMEDLKYWLDEFGndPELVKEALKEAVSNNkANYKYIDAILNNWKNNGIKTVEDVEA 73
DnaB_2 pfam07261
Replication initiation and membrane attachment; This family consists of several bacterial ...
 173-238 6.99e-10

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: 54.08  E-value: 6.99e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070099596 173 LYQTNFG-IVKPILYDDLKADLKDYGL--ELIIEAVKRAVKRQ-REYAYAQGILKSWNRSGIKTLEQAKA 238
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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