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Conserved domains on  [gi|2458220687|ref|WP_275592006|]
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single-stranded DNA-binding protein [Campylobacter sp. RM12651]

Protein Classification

single-stranded DNA-binding protein( domain architecture ID 10139633)

single-stranded DNA (ssDNA)-binding protein plays a key role in DNA replication, recombination, and repair

CATH:  2.40.50.140
Gene Ontology:  GO:0003697|GO:0006260
PubMed:  27838363
SCOP:  4000346

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 4-102 3.41e-20

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: 78.81  E-value: 3.41e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2458220687   4 CNFTGRLVNEV-MLHTKGQTMWINNTLAIYNRKKVDERWEEDTIFIEFSAFGKNAEMINKYTRKGDRISLIGKITQERWV 82
Cdd:cd04496     1 VILIGRLGKDPeLRYTPSGTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRSWE 80

                          90       100
                  ....*....|....*....|
gi 2458220687  83 DKNNNNRTQLKLLVEKIYLI 102
Cdd:cd04496    81 DKDGQKRYGTEVVADRIEFL 100
 
Name Accession Description Interval E-value
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 4-102 3.41e-20

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: 78.81  E-value: 3.41e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2458220687   4 CNFTGRLVNEV-MLHTKGQTMWINNTLAIYNRKKVDERWEEDTIFIEFSAFGKNAEMINKYTRKGDRISLIGKITQERWV 82
Cdd:cd04496     1 VILIGRLGKDPeLRYTPSGTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRSWE 80

                          90       100
                  ....*....|....*....|
gi 2458220687  83 DKNNNNRTQLKLLVEKIYLI 102
Cdd:cd04496    81 DKDGQKRYGTEVVADRIEFL 100
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
1-104 2.38e-19

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 76.80  E-value: 2.38e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2458220687   1 MNVCNFTGRLVNEV-MLHTKGQTMWINNTLAI-YNRKKVDERWEEDTIFIEFSAFGKNAEMINKYTRKGDRISLIGKITQ 78
Cdd:COG0629     1 MNKVTLVGRLGKDPeLRYTPSGTAVANFRLAVnRRYKDQDGEWKDETDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRT 80

                          90       100
                  ....*....|....*....|....*.
gi 2458220687  79 ERWVDKNNNNRTQLKLLVEKIYLIDY 104
Cdd:COG0629    81 RSWEDKDGQKRYTTEVVADEIQFLGS 106
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 7-102 7.55e-14

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: 62.64  E-value: 7.55e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2458220687   7 TGRLVNEVMLH-TKGQTMWINNTLAIYNRKKVDERWEEDTIFIEFSAFGKNAEMINKYTRKGDRISLIGKITQERWVDKN 85
Cdd:pfam00436   7 VGRLTRDPELRyTPNGNAVANFTLATNRRFKDRGEGDEETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLQTRKYEDQE 86

                          90
                  ....*....|....*..
gi 2458220687  86 NNNRTQLKLLVEKIYLI 102
Cdd:pfam00436  87 GQKRYVTEIVADEVQFL 103
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 8-116 2.41e-13

single stranded DNA-binding protein (ssb); All proteins in this family for which functions are known are single-stranded DNA binding proteins that function in many processes including transcription, repair, replication and recombination. Members encoded between genes for ribosomal proteins S6 and S18 should be annotated as primosomal protein N (PriB). Forms in gamma-protoeobacteria are much shorter and poorly recognized by this model. Additional members of this family include phage proteins. Eukaryotic members are organellar proteins. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273179 [Multi-domain]  Cd Length: 164  Bit Score: 62.82  E-value: 2.41e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2458220687   8 GRLVNE-VMLHTKGQTMWINNTLAIYNR-KKVDERWEEDTIFIEFSAFGKNAEMINKYTRKGDRISLIGKITQERWVDKN 85
Cdd:TIGR00621  11 GRLTRDpELRYTPSGNAVANFTLATNRRwKDQDGEWKEETEWHDIVIFGRLAEVAAQYLKKGSLVYVEGRLRTRKWEDQN 90

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2458220687  86 NNNRTQLKLLVEKIYLIDYIKPDTNKNSIEN 116
Cdd:TIGR00621  91 GQKRSKTEIIADNVQLLDLLGARAQGGEFSG 121
PRK08486 PRK08486
single-stranded DNA-binding protein; Provisional
 35-122 6.53e-11

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236275 [Multi-domain]  Cd Length: 182  Bit Score: 56.78  E-value: 6.53e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2458220687  35 KKVDERWEEDTIFIEFSAFGKNAEMINKYTRKGDRISLIGKITQERWVDKNNNNRTQLKLLVEKIYLIDyikpDTNKNSI 114
Cdd:PRK08486   38 KKQDGEKGEEVCFIDIRLFGRTAEIANQYLSKGSKVLIEGRLTFESWMDQNGQKRSKHTITAESMQMLD----SKSDNPQ 113


                  ....*...
gi 2458220687 115 ENINDEDS 122
Cdd:PRK08486  114 ANAMQDNS 121
 
Name Accession Description Interval E-value
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 4-102 3.41e-20

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: 78.81  E-value: 3.41e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2458220687   4 CNFTGRLVNEV-MLHTKGQTMWINNTLAIYNRKKVDERWEEDTIFIEFSAFGKNAEMINKYTRKGDRISLIGKITQERWV 82
Cdd:cd04496     1 VILIGRLGKDPeLRYTPSGTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRSWE 80

                          90       100
                  ....*....|....*....|
gi 2458220687  83 DKNNNNRTQLKLLVEKIYLI 102
Cdd:cd04496    81 DKDGQKRYGTEVVADRIEFL 100
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
1-104 2.38e-19

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 76.80  E-value: 2.38e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2458220687   1 MNVCNFTGRLVNEV-MLHTKGQTMWINNTLAI-YNRKKVDERWEEDTIFIEFSAFGKNAEMINKYTRKGDRISLIGKITQ 78
Cdd:COG0629     1 MNKVTLVGRLGKDPeLRYTPSGTAVANFRLAVnRRYKDQDGEWKDETDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRT 80

                          90       100
                  ....*....|....*....|....*.
gi 2458220687  79 ERWVDKNNNNRTQLKLLVEKIYLIDY 104
Cdd:COG0629    81 RSWEDKDGQKRYTTEVVADEIQFLGS 106
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 7-102 7.55e-14

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: 62.64  E-value: 7.55e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2458220687   7 TGRLVNEVMLH-TKGQTMWINNTLAIYNRKKVDERWEEDTIFIEFSAFGKNAEMINKYTRKGDRISLIGKITQERWVDKN 85
Cdd:pfam00436   7 VGRLTRDPELRyTPNGNAVANFTLATNRRFKDRGEGDEETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLQTRKYEDQE 86

                          90
                  ....*....|....*..
gi 2458220687  86 NNNRTQLKLLVEKIYLI 102
Cdd:pfam00436  87 GQKRYVTEIVADEVQFL 103
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 8-116 2.41e-13

single stranded DNA-binding protein (ssb); All proteins in this family for which functions are known are single-stranded DNA binding proteins that function in many processes including transcription, repair, replication and recombination. Members encoded between genes for ribosomal proteins S6 and S18 should be annotated as primosomal protein N (PriB). Forms in gamma-protoeobacteria are much shorter and poorly recognized by this model. Additional members of this family include phage proteins. Eukaryotic members are organellar proteins. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273179 [Multi-domain]  Cd Length: 164  Bit Score: 62.82  E-value: 2.41e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2458220687   8 GRLVNE-VMLHTKGQTMWINNTLAIYNR-KKVDERWEEDTIFIEFSAFGKNAEMINKYTRKGDRISLIGKITQERWVDKN 85
Cdd:TIGR00621  11 GRLTRDpELRYTPSGNAVANFTLATNRRwKDQDGEWKEETEWHDIVIFGRLAEVAAQYLKKGSLVYVEGRLRTRKWEDQN 90

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2458220687  86 NNNRTQLKLLVEKIYLIDYIKPDTNKNSIEN 116
Cdd:TIGR00621  91 GQKRSKTEIIADNVQLLDLLGARAQGGEFSG 121
PRK08486 PRK08486
single-stranded DNA-binding protein; Provisional
 35-122 6.53e-11

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236275 [Multi-domain]  Cd Length: 182  Bit Score: 56.78  E-value: 6.53e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2458220687  35 KKVDERWEEDTIFIEFSAFGKNAEMINKYTRKGDRISLIGKITQERWVDKNNNNRTQLKLLVEKIYLIDyikpDTNKNSI 114
Cdd:PRK08486   38 KKQDGEKGEEVCFIDIRLFGRTAEIANQYLSKGSKVLIEGRLTFESWMDQNGQKRSKHTITAESMQMLD----SKSDNPQ 113


                  ....*...
gi 2458220687 115 ENINDEDS 122
Cdd:PRK08486  114 ANAMQDNS 121
PRK07459 PRK07459
single-stranded DNA-binding protein; Provisional
 26-126 9.51e-06

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180986  Cd Length: 121  Bit Score: 41.60  E-value: 9.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2458220687  26 NNTLAIYNRKKVDErweEDTIFIEFsaFGKNAEMINKYTRKGDRISLIGKITQERWVDKNNN-NRTQLKLLVEKIYLIDY 104
Cdd:PRK07459   29 NLTLAVNRRSRDDE---PDWFNLEI--WGKTAQVAADYVKKGSLIGITGSLKFDRWTDRNTGeDRSKPVIRVDRLELLGS 103

                          90       100
                  ....*....|....*....|..
gi 2458220687 105 iKPDTNKNsieNINDEDSEIPF 126
Cdd:PRK07459  104 -KRDSEGN---ANPSNSSEIPF 121
PRK07274 PRK07274
single-stranded DNA-binding protein; Provisional
 1-126 3.35e-04

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180914  Cd Length: 131  Bit Score: 37.82  E-value: 3.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2458220687   1 MNVCNFTGRLVNEVMLH-TKGQTMWINNTLAIyNRKKVDERWEEDTIFIEFSAFGKNAEMINKYTRKGDRISLIGKITQE 79
Cdd:PRK07274    2 YNKVILIGRLTATPELVkTANDKSVARVTLAV-NRRFKNQNGEREADFINVVLWGKLAETLASYASKGSLISIDGELRTR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2458220687  80 RWvDKNNNNRTQLKLLVEKIYLIDY-----IKPDTNKNSIENINDEDSEIPF 126
Cdd:PRK07274   81 KY-EKDGQTHYVTEVLCQSFQLLESraqraMRENNVGNDLADLVLEEEELPF 131
PRK06752 PRK06752
single-stranded DNA-binding protein; Validated
 1-103 2.08e-03

single-stranded DNA-binding protein; Validated


Pssm-ID: 168660  Cd Length: 112  Bit Score: 35.40  E-value: 2.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2458220687   1 MNVCNFTGRLVNEVMLHTKGQTMWINNTLAIYNRKKVDERWEEDTIFIEFSAFGKNAEMINKYTRKGDRISLIGKITQER 80
Cdd:PRK06752    2 MNRVVLIGRLTKEPELYYTKQGVAYARVCVAVNRGFRNSLGEQQVDFINCVVWRKSAENVTEYCTKGSLVGITGRIHTRN 81

                          90       100
                  ....*....|....*....|...
gi 2458220687  81 WVDKNNNNRTQLKLLVEKIYLID 103
Cdd:PRK06752   82 YEDDQGKRIYITEVVIESITFLE 104
PRK06958 PRK06958
single-stranded DNA-binding protein; Provisional
 53-89 6.63e-03

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180777 [Multi-domain]  Cd Length: 182  Bit Score: 34.77  E-value: 6.63e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2458220687  53 FGKNAEMINKYTRKGDRISLIGKITQERWVDKNNNNR 89
Cdd:PRK06958   59 FGRLAEIVGEYLKKGSSVYIEGRIRTRKWQGQDGQDR 95
 
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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