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Conserved domains on  [gi|1608031042|gb|TFY49889|]
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primosomal replication protein N [Escherichia coli]

Protein Classification

primosomal replication protein N( domain architecture ID 10006819)

primosomal replication protein N (PriB) is one of three proteins involved in the PriA-dependent replication restart system which participate in the reconstruction of the replisome by further stabilizing the PriA-DNA complex and stimulating PriA helicase activity.

Gene Ontology:  GO:1990158|GO:0006268
PubMed:  29202195

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PriB COG2965
Primosomal replication protein N [Replication, recombination and repair];
1-101 1.31e-48

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


:

Pssm-ID: 442205  Cd Length: 98  Bit Score: 149.57  E-value: 1.31e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608031042   1 MTNRLVLSGTVCRTPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGhENQAITHSITVGSRITVQGFISC 80
Cdd:COG2965     1 MMNRLVLSGTVVERPALRYTPAGIPVLEFVLEHRSEQQEAGLPRQVECEIPAVASG-ELAEKLARLPLGSQVRVTGFLAR 79

                          90       100
                  ....*....|....*....|.
gi 1608031042  81 HkaKNGLSKMVLHAEQIELID 101
Cdd:COG2965    80 K--SRGSRQLVLHIQQIELID 98
 
Name Accession Description Interval E-value
PriB COG2965
Primosomal replication protein N [Replication, recombination and repair];
1-101 1.31e-48

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


Pssm-ID: 442205  Cd Length: 98  Bit Score: 149.57  E-value: 1.31e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608031042   1 MTNRLVLSGTVCRTPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGhENQAITHSITVGSRITVQGFISC 80
Cdd:COG2965     1 MMNRLVLSGTVVERPALRYTPAGIPVLEFVLEHRSEQQEAGLPRQVECEIPAVASG-ELAEKLARLPLGSQVRVTGFLAR 79

                          90       100
                  ....*....|....*....|.
gi 1608031042  81 HkaKNGLSKMVLHAEQIELID 101
Cdd:COG2965    80 K--SRGSRQLVLHIQQIELID 98
PriB_gamma TIGR04418
primosomal replication protein PriB; Members of this protein family are primosomal replication ...
 3-100 4.93e-46

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: 143.11  E-value: 4.93e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608031042   3 NRLVLSGTVCRTPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGhENQAITHSITVGSRITVQGFISCHK 82
Cdd:TIGR04418   1 NRLVLSGTVAETPKLRYTPAGIPHLEFVLEHRSQQEEAGQPRQVECEIQAVASG-ELAEKLARLTVGSRVRVTGFLARKS 79

                          90
                  ....*....|....*...
gi 1608031042  83 AKNGLsKMVLHAEQIELI 100
Cdd:TIGR04418  80 HRNGL-QLVLHAQQIEFI 96
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 3-100 1.49e-15

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: 66.10  E-value: 1.49e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608031042   3 NRLVLSGTVCRTPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHK 82
Cdd:pfam00436   2 NKVILVGRLTRDPELRYTPNGNAVANFTLATNRRFKDRGEGDEETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLQTRK 81

                          90       100
                  ....*....|....*....|..
gi 1608031042  83 --AKNGLSKMV--LHAEQIELI 100
Cdd:pfam00436  82 yeDQEGQKRYVteIVADEVQFL 103
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 6-100 2.35e-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: 60.32  E-value: 2.35e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608031042   6 VLSGTVCRTPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHK--A 83
Cdd:cd04496     2 ILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRSweD 81

                          90
                  ....*....|....*....
gi 1608031042  84 KNGL--SKMVLHAEQIELI 100
Cdd:cd04496    82 KDGQkrYGTEVVADRIEFL 100
 
Name Accession Description Interval E-value
PriB COG2965
Primosomal replication protein N [Replication, recombination and repair];
1-101 1.31e-48

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


Pssm-ID: 442205  Cd Length: 98  Bit Score: 149.57  E-value: 1.31e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608031042   1 MTNRLVLSGTVCRTPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGhENQAITHSITVGSRITVQGFISC 80
Cdd:COG2965     1 MMNRLVLSGTVVERPALRYTPAGIPVLEFVLEHRSEQQEAGLPRQVECEIPAVASG-ELAEKLARLPLGSQVRVTGFLAR 79

                          90       100
                  ....*....|....*....|.
gi 1608031042  81 HkaKNGLSKMVLHAEQIELID 101
Cdd:COG2965    80 K--SRGSRQLVLHIQQIELID 98
PriB_gamma TIGR04418
primosomal replication protein PriB; Members of this protein family are primosomal replication ...
 3-100 4.93e-46

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: 143.11  E-value: 4.93e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608031042   3 NRLVLSGTVCRTPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGhENQAITHSITVGSRITVQGFISCHK 82
Cdd:TIGR04418   1 NRLVLSGTVAETPKLRYTPAGIPHLEFVLEHRSQQEEAGQPRQVECEIQAVASG-ELAEKLARLTVGSRVRVTGFLARKS 79

                          90
                  ....*....|....*...
gi 1608031042  83 AKNGLsKMVLHAEQIELI 100
Cdd:TIGR04418  80 HRNGL-QLVLHAQQIEFI 96
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 3-100 1.49e-15

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: 66.10  E-value: 1.49e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608031042   3 NRLVLSGTVCRTPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHK 82
Cdd:pfam00436   2 NKVILVGRLTRDPELRYTPNGNAVANFTLATNRRFKDRGEGDEETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLQTRK 81

                          90       100
                  ....*....|....*....|..
gi 1608031042  83 --AKNGLSKMV--LHAEQIELI 100
Cdd:pfam00436  82 yeDQEGQKRYVteIVADEVQFL 103
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 6-100 2.35e-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: 60.32  E-value: 2.35e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608031042   6 VLSGTVCRTPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHK--A 83
Cdd:cd04496     2 ILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRSweD 81

                          90
                  ....*....|....*....
gi 1608031042  84 KNGL--SKMVLHAEQIELI 100
Cdd:cd04496    82 KDGQkrYGTEVVADRIEFL 100
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
3-102 1.43e-04

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 37.90  E-value: 1.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608031042   3 NRLVLSGTVCRTPLRKVSPSGIPHCQFVL--------EHRSVQEEAGFHRqawcqmpVIVSGHENQAITHSITVGSRITV 74
Cdd:COG0629     2 NKVTLVGRLGKDPELRYTPSGTAVANFRLavnrrykdQDGEWKDETDWHR-------VVAWGKLAENAAEYLKKGDKVYV 74

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1608031042  75 QGFISCHK--AKNGL--SKMVLHAEQIELIDS 102
Cdd:COG0629    75 EGRLRTRSweDKDGQkrYTTEVVADEIQFLGS 106
 
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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