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Conserved domains on  [gi|490725941|ref|WP_004588456|]
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MULTISPECIES: primosomal replication protein N [Pseudoalteromonas]

Protein Classification

primosomal replication protein N( domain architecture ID 10025198)

primosomal replication protein N binds single-stranded DNA at the primosome assembly site (PAS)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PriB_gamma TIGR04418
primosomal replication protein PriB; Members of this protein family are primosomal replication ...
 7-104 1.83e-41

primosomal replication protein PriB; Members of this protein family are primosomal replication protein N (PriB), virtually always encoded between rpsF (ribosomal protein S6) and rpsR (ribosomal protein S18). Note that only this short form, as found primarily in the gamma-Proteobacteria, of the single-stranded DNA binding protein family (see model TIGR00621) may partner with PriA and be involved in priming for re-initiation of replication. [DNA metabolism, DNA replication, recombination, and repair]


:

Pssm-ID: 275211  Cd Length: 96  Bit Score: 131.56  E-value: 1.83e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490725941    7 NQLVISGVVCKTPKFSQSPAGIPHCIFVVEHKSMQTEADLNRNSYVRLQVVASGkQMQQQTQHLHVGQALQVSGFLNRHE 86
Cdd:TIGR04418   1 NRLVLSGTVAETPKLRYTPAGIPHLEFVLEHRSQQEEAGQPRQVECEIQAVASG-ELAEKLARLTVGSRVRVTGFLARKS 79

                          90
                  ....*....|....*...
gi 490725941   87 GRNGLsQLVLHAQHIERI 104
Cdd:TIGR04418  80 HRNGL-QLVLHAQQIEFI 96
 
Name Accession Description Interval E-value
PriB_gamma TIGR04418
primosomal replication protein PriB; Members of this protein family are primosomal replication ...
 7-104 1.83e-41

primosomal replication protein PriB; Members of this protein family are primosomal replication protein N (PriB), virtually always encoded between rpsF (ribosomal protein S6) and rpsR (ribosomal protein S18). Note that only this short form, as found primarily in the gamma-Proteobacteria, of the single-stranded DNA binding protein family (see model TIGR00621) may partner with PriA and be involved in priming for re-initiation of replication. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 275211  Cd Length: 96  Bit Score: 131.56  E-value: 1.83e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490725941    7 NQLVISGVVCKTPKFSQSPAGIPHCIFVVEHKSMQTEADLNRNSYVRLQVVASGkQMQQQTQHLHVGQALQVSGFLNRHE 86
Cdd:TIGR04418   1 NRLVLSGTVAETPKLRYTPAGIPHLEFVLEHRSQQEEAGQPRQVECEIQAVASG-ELAEKLARLTVGSRVRVTGFLARKS 79

                          90
                  ....*....|....*...
gi 490725941   87 GRNGLsQLVLHAQHIERI 104
Cdd:TIGR04418  80 HRNGL-QLVLHAQQIEFI 96
PriB COG2965
Primosomal replication protein N [Replication, recombination and repair];
6-104 1.36e-40

Primosomal replication protein N [Replication, recombination and repair];


Pssm-ID: 442205  Cd Length: 98  Bit Score: 129.54  E-value: 1.36e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490725941   6 MNQLVISGVVCKTPKFSQSPAGIPHCIFVVEHKSMQTEADLNRNSYVRLQVVASGkQMQQQTQHLHVGQALQVSGFLNRH 85
Cdd:COG2965    2 MNRLVLSGTVVERPALRYTPAGIPVLEFVLEHRSEQQEAGLPRQVECEIPAVASG-ELAEKLARLPLGSQVRVTGFLARK 80

                         90
                 ....*....|....*....
gi 490725941  86 egRNGLSQLVLHAQHIERI 104
Cdd:COG2965   81 --SRGSRQLVLHIQQIELI 97
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 10-104 7.10e-13

SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart at forks that have stalled at sites of DNA damage. It also plays a role in the assembly of primosome during replication initiation at the bacteriophage phiX174 origin. PriB physically interacts with SSB and binds ssDNA with high affinity.


Pssm-ID: 239942  Cd Length: 100  Bit Score: 59.16  E-value: 7.10e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490725941  10 VISGVVCKTPKFSQSPAGIPHCIFVVEHKSMQTEADLNRNSYVRLQVVASGKQMQQQTQHLHVGQALQVSGFL--NRHEG 87
Cdd:cd04496    2 ILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLrtRSWED 81

                         90
                 ....*....|....*....
gi 490725941  88 RNGL--SQLVLHAQHIERI 104
Cdd:cd04496   82 KDGQkrYGTEVVADRIEFL 100
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 6-104 1.66e-11

Single-strand binding protein family; This family includes single stranded binding proteins and also the primosomal replication protein N (PriB). PriB forms a complex with PriA, PriC and ssDNA.


Pssm-ID: 425680  Cd Length: 103  Bit Score: 55.70  E-value: 1.66e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490725941    6 MNQLVISGVVCKTPKFSQSPAGIPHCIFVVEHKSMQTEADLNRNSYVRLQVVASGKQMQQQTQHLHVGQALQVSGFL--N 83
Cdd:pfam00436   1 MNKVILVGRLTRDPELRYTPNGNAVANFTLATNRRFKDRGEGDEETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLqtR 80

                          90       100
                  ....*....|....*....|...
gi 490725941   84 RHEGRNGL--SQLVLHAQHIERI 104
Cdd:pfam00436  81 KYEDQEGQkrYVTEIVADEVQFL 103
 
Name Accession Description Interval E-value
PriB_gamma TIGR04418
primosomal replication protein PriB; Members of this protein family are primosomal replication ...
 7-104 1.83e-41

primosomal replication protein PriB; Members of this protein family are primosomal replication protein N (PriB), virtually always encoded between rpsF (ribosomal protein S6) and rpsR (ribosomal protein S18). Note that only this short form, as found primarily in the gamma-Proteobacteria, of the single-stranded DNA binding protein family (see model TIGR00621) may partner with PriA and be involved in priming for re-initiation of replication. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 275211  Cd Length: 96  Bit Score: 131.56  E-value: 1.83e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490725941    7 NQLVISGVVCKTPKFSQSPAGIPHCIFVVEHKSMQTEADLNRNSYVRLQVVASGkQMQQQTQHLHVGQALQVSGFLNRHE 86
Cdd:TIGR04418   1 NRLVLSGTVAETPKLRYTPAGIPHLEFVLEHRSQQEEAGQPRQVECEIQAVASG-ELAEKLARLTVGSRVRVTGFLARKS 79

                          90
                  ....*....|....*...
gi 490725941   87 GRNGLsQLVLHAQHIERI 104
Cdd:TIGR04418  80 HRNGL-QLVLHAQQIEFI 96
PriB COG2965
Primosomal replication protein N [Replication, recombination and repair];
6-104 1.36e-40

Primosomal replication protein N [Replication, recombination and repair];


Pssm-ID: 442205  Cd Length: 98  Bit Score: 129.54  E-value: 1.36e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490725941   6 MNQLVISGVVCKTPKFSQSPAGIPHCIFVVEHKSMQTEADLNRNSYVRLQVVASGkQMQQQTQHLHVGQALQVSGFLNRH 85
Cdd:COG2965    2 MNRLVLSGTVVERPALRYTPAGIPVLEFVLEHRSEQQEAGLPRQVECEIPAVASG-ELAEKLARLPLGSQVRVTGFLARK 80

                         90
                 ....*....|....*....
gi 490725941  86 egRNGLSQLVLHAQHIERI 104
Cdd:COG2965   81 --SRGSRQLVLHIQQIELI 97
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 10-104 7.10e-13

SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart at forks that have stalled at sites of DNA damage. It also plays a role in the assembly of primosome during replication initiation at the bacteriophage phiX174 origin. PriB physically interacts with SSB and binds ssDNA with high affinity.


Pssm-ID: 239942  Cd Length: 100  Bit Score: 59.16  E-value: 7.10e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490725941  10 VISGVVCKTPKFSQSPAGIPHCIFVVEHKSMQTEADLNRNSYVRLQVVASGKQMQQQTQHLHVGQALQVSGFL--NRHEG 87
Cdd:cd04496    2 ILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLrtRSWED 81

                         90
                 ....*....|....*....
gi 490725941  88 RNGL--SQLVLHAQHIERI 104
Cdd:cd04496   82 KDGQkrYGTEVVADRIEFL 100
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 6-104 1.66e-11

Single-strand binding protein family; This family includes single stranded binding proteins and also the primosomal replication protein N (PriB). PriB forms a complex with PriA, PriC and ssDNA.


Pssm-ID: 425680  Cd Length: 103  Bit Score: 55.70  E-value: 1.66e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490725941    6 MNQLVISGVVCKTPKFSQSPAGIPHCIFVVEHKSMQTEADLNRNSYVRLQVVASGKQMQQQTQHLHVGQALQVSGFL--N 83
Cdd:pfam00436   1 MNKVILVGRLTRDPELRYTPNGNAVANFTLATNRRFKDRGEGDEETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLqtR 80

                          90       100
                  ....*....|....*....|...
gi 490725941   84 RHEGRNGL--SQLVLHAQHIERI 104
Cdd:pfam00436  81 KYEDQEGQkrYVTEIVADEVQFL 103
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
6-90 3.02e-03

Single-stranded DNA-binding protein [Replication, recombination and repair];


Pssm-ID: 440394  Cd Length: 116  Bit Score: 34.43  E-value: 3.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490725941   6 MNQLVISGVVCKTPKFSQSPAGIPHCIFVV---EHKSMQTEADLNRNSYVRlqVVASGKQMQQQTQHLHVGQALQVSGFL 82
Cdd:COG0629    1 MNKVTLVGRLGKDPELRYTPSGTAVANFRLavnRRYKDQDGEWKDETDWHR--VVAWGKLAENAAEYLKKGDKVYVEGRL 78

                         90
                 ....*....|
gi 490725941  83 --NRHEGRNG 90
Cdd:COG0629   79 rtRSWEDKDG 88
tRNA_anti-codon pfam01336
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
 53-104 7.16e-03

OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.


Pssm-ID: 460164 [Multi-domain]  Cd Length: 75  Bit Score: 32.59  E-value: 7.16e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 490725941   53 RLQVVASGKQMQQQTQHLHVGQALQVSGFLNRHEGRnglsQLVLHAQHIERI 104
Cdd:pfam01336  28 SIQVVVFKEEAEKLAKKLKEGDVVRVTGKVKKRKGG----ELELVVEEIELL 75
 
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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