NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2627794092|ref|WP_320859694|]
View 

phage replisome organizer N-terminal domain-containing protein [Clostridium tertium]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 6-125 1.11e-44

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 pfam09681:

Pssm-ID: 447848  Cd Length: 121  Bit Score: 146.38  E-value: 1.11e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2627794092   6 WIKLNTDMFDNAKIKYLRTLPEGDKIVLIWVMLLAKAGKCNANGYIFLTENIPYTQDMLAAEFDFEITTIQLALTSLMRL 85
Cdd:pfam09681   1 WIKLKVNMFDDEKIKLIEKMPEGDTYIVIWLKLLLLSGKTNNNGYIMLSENIPYTAEMLATIFNRPLNTVRLALQTFKQF 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2627794092  86 GMINLDESNL-YVTGWEEHQNIEGLEKIREQNRKRVAKYRE 125
Cdd:pfam09681  81 GMIEISDNGAiKITNWSKHQNLESLEKHRERTRRRKQKHRE 121
DnaB_2 super family cl29255
Replication initiation and membrane attachment; This family consists of several bacterial ...
 186-255 1.45e-07

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.


The actual alignment was detected with superfamily member COG3935:

Pssm-ID: 475170  Cd Length: 103  Bit Score: 48.47  E-value: 1.45e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2627794092 186 GTLNKTLLDKLLADVEI--YSIEWVTKAIEIGNQRSKRTYSYLKGILENWKTEGIKN-QKGKNEIQERIEKGE 255
Cdd:COG3935    11 RPLSPFEIEKINKWLDEdgFSPELILEALKEAVENGKRNFKYIDRILKNWKKKGIKTvEDAEAYEKKFKKRKK 83
 
Name Accession Description Interval E-value
Phage_rep_org_N pfam09681
N-terminal phage replisome organizer (Phage_rep_org_N); This entry represents the N-terminal ...
 6-125 1.11e-44

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: 146.38  E-value: 1.11e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2627794092   6 WIKLNTDMFDNAKIKYLRTLPEGDKIVLIWVMLLAKAGKCNANGYIFLTENIPYTQDMLAAEFDFEITTIQLALTSLMRL 85
Cdd:pfam09681   1 WIKLKVNMFDDEKIKLIEKMPEGDTYIVIWLKLLLLSGKTNNNGYIMLSENIPYTAEMLATIFNRPLNTVRLALQTFKQF 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2627794092  86 GMINLDESNL-YVTGWEEHQNIEGLEKIREQNRKRVAKYRE 125
Cdd:pfam09681  81 GMIEISDNGAiKITNWSKHQNLESLEKHRERTRRRKQKHRE 121
phage_rep_org_N TIGR01714
phage replisome organizer, putative, N-terminal region; This model represents the N-terminal ...
 6-125 6.42e-30

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: 108.35  E-value: 6.42e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2627794092   6 WIKLNTDMFDNAKIKYLRTLPEGDKIVLIWVMLLAKAgkCNANGYIFLTENIPYTQDMLAAEFDFEITTIQLALTSLMRL 85
Cdd:TIGR01714   1 WIKLKVNFFDSKEIKLLEKMPEGDTHTIIWLKLLLLS--LNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLESL 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2627794092  86 GMIN-LDESNLYVTGWEEHQNIEGLEKIREQNRKRVAKYRE 125
Cdd:TIGR01714  79 GLIEkKNNGDIFLENWEKHVGSDSASARRERKFRRNQKALE 119
DnaD COG3935
DNA replication protein DnaD [Replication, recombination and repair];
186-255 1.45e-07

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


Pssm-ID: 443136  Cd Length: 103  Bit Score: 48.47  E-value: 1.45e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2627794092 186 GTLNKTLLDKLLADVEI--YSIEWVTKAIEIGNQRSKRTYSYLKGILENWKTEGIKN-QKGKNEIQERIEKGE 255
Cdd:COG3935    11 RPLSPFEIEKINKWLDEdgFSPELILEALKEAVENGKRNFKYIDRILKNWKKKGIKTvEDAEAYEKKFKKRKK 83
DnaD_dom TIGR01446
DnaD and phage-associated domain; This model represents the conserved domain of DnaD, part of ...
 180-239 4.67e-05

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: 40.75  E-value: 4.67e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2627794092 180 WTSNGYGTLNKTLLDKLLADVE--IYSIEWVTKAIEIGNQRSKRTYSYLKGILENWKTEGIK 239
Cdd:TIGR01446   5 FEENFGRMLSPFEMEDLKYWLDefGNDPELVKEALKEAVSNNKANYKYIDAILNNWKNNGIK 66
 
Name Accession Description Interval E-value
Phage_rep_org_N pfam09681
N-terminal phage replisome organizer (Phage_rep_org_N); This entry represents the N-terminal ...
 6-125 1.11e-44

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: 146.38  E-value: 1.11e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2627794092   6 WIKLNTDMFDNAKIKYLRTLPEGDKIVLIWVMLLAKAGKCNANGYIFLTENIPYTQDMLAAEFDFEITTIQLALTSLMRL 85
Cdd:pfam09681   1 WIKLKVNMFDDEKIKLIEKMPEGDTYIVIWLKLLLLSGKTNNNGYIMLSENIPYTAEMLATIFNRPLNTVRLALQTFKQF 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2627794092  86 GMINLDESNL-YVTGWEEHQNIEGLEKIREQNRKRVAKYRE 125
Cdd:pfam09681  81 GMIEISDNGAiKITNWSKHQNLESLEKHRERTRRRKQKHRE 121
phage_rep_org_N TIGR01714
phage replisome organizer, putative, N-terminal region; This model represents the N-terminal ...
 6-125 6.42e-30

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: 108.35  E-value: 6.42e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2627794092   6 WIKLNTDMFDNAKIKYLRTLPEGDKIVLIWVMLLAKAgkCNANGYIFLTENIPYTQDMLAAEFDFEITTIQLALTSLMRL 85
Cdd:TIGR01714   1 WIKLKVNFFDSKEIKLLEKMPEGDTHTIIWLKLLLLS--LNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLESL 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2627794092  86 GMIN-LDESNLYVTGWEEHQNIEGLEKIREQNRKRVAKYRE 125
Cdd:TIGR01714  79 GLIEkKNNGDIFLENWEKHVGSDSASARRERKFRRNQKALE 119
DnaD COG3935
DNA replication protein DnaD [Replication, recombination and repair];
186-255 1.45e-07

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


Pssm-ID: 443136  Cd Length: 103  Bit Score: 48.47  E-value: 1.45e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2627794092 186 GTLNKTLLDKLLADVEI--YSIEWVTKAIEIGNQRSKRTYSYLKGILENWKTEGIKN-QKGKNEIQERIEKGE 255
Cdd:COG3935    11 RPLSPFEIEKINKWLDEdgFSPELILEALKEAVENGKRNFKYIDRILKNWKKKGIKTvEDAEAYEKKFKKRKK 83
DnaD_dom TIGR01446
DnaD and phage-associated domain; This model represents the conserved domain of DnaD, part of ...
 180-239 4.67e-05

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: 40.75  E-value: 4.67e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2627794092 180 WTSNGYGTLNKTLLDKLLADVE--IYSIEWVTKAIEIGNQRSKRTYSYLKGILENWKTEGIK 239
Cdd:TIGR01446   5 FEENFGRMLSPFEMEDLKYWLDefGNDPELVKEALKEAVSNNKANYKYIDAILNNWKNNGIK 66
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH