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Conserved domains on  [gi|918234684|ref|WP_052366665|]
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single-stranded DNA-binding protein [Bifidobacterium tsurumiense]

Protein Classification

single-stranded DNA-binding protein( domain architecture ID 11427956)

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:  12598368|8458342|27838363
SCOP:  4000346

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
10-91 3.52e-21

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


:

Pssm-ID: 440394  Cd Length: 116  Bit Score: 84.12  E-value: 3.52e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 918234684  10 CSFRIGSTRSYYQASsNQWHEhPTTWITVKTFRNLATNTRMSIHKGDPVIVTGVLNTEEWV-QDGNKRSRMVVEASSIGH 88
Cdd:COG0629   26 ANFRLAVNRRYKDQD-GEWKD-ETDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRTRSWEdKDGQKRYTTEVVADEIQF 103


                 ...
gi 918234684  89 DLS 91
Cdd:COG0629  104 LGS 106
 
Name Accession Description Interval E-value
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
10-91 3.52e-21

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 84.12  E-value: 3.52e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 918234684  10 CSFRIGSTRSYYQASsNQWHEhPTTWITVKTFRNLATNTRMSIHKGDPVIVTGVLNTEEWV-QDGNKRSRMVVEASSIGH 88
Cdd:COG0629   26 ANFRLAVNRRYKDQD-GEWKD-ETDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRTRSWEdKDGQKRYTTEVVADEIQF 103


                 ...
gi 918234684  89 DLS 91
Cdd:COG0629  104 LGS 106
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 10-89 1.87e-16

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: 71.49  E-value: 1.87e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 918234684  10 CSFRIGSTRSYYqasSNQWHEHPTTWITVKTFRNLATNTRMSIHKGDPVIVTGVLNTEEWV-QDGNKRSRMVVEASSIGH 88
Cdd:cd04496   23 ARFSLAVNRRRK---DRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRSWEdKDGQKRYGTEVVADRIEF 99


                 .
gi 918234684  89 D 89
Cdd:cd04496  100 L 100
PRK07772 PRK07772
single-stranded DNA-binding protein; Provisional
 10-166 1.14e-13

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236092 [Multi-domain]  Cd Length: 186  Bit Score: 66.21  E-value: 1.14e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 918234684  10 CSFRIGSTRSYYQASSNQWHEHPTTWITVKTFRNLATNTRMSIHKGDPVIVTGVLNTEEW-VQDGNKRSRMVVEASSIGH 88
Cdd:PRK07772  29 ANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIVTGRLKQRSYeTREGEKRTVVELEVDEIGP 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 918234684  89 DLSMGYSQFTRLKSGDpvmaeRNARRSVGFVGA--DSSGKDAGPQSRQQENSDGNQAESLGVDPWNGDEGVGGQNAVTSE 166
Cdd:PRK07772 109 SLRYATAKVTRASRGG-----GGGGGGGGFGGGggGSGGGGGGGGGGGAPGGGGAQASAPADDPWSSAPASGGFGGGDDE 183
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 10-89 1.84e-10

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: 1.84e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 918234684   10 CSFRIGSTRSYyqaSSNQWHEHPTTWITVKTFRNLATNTRMSIHKGDPVIVTGVLNTEEW-VQDGNKRSRMVVEASSIGH 88
Cdd:pfam00436  26 ANFTLATNRRF---KDRGEGDEETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLQTRKYeDQEGQKRYVTEIVADEVQF 102


                  .
gi 918234684   89 D 89
Cdd:pfam00436 103 L 103
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 7-155 2.73e-07

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: 48.18  E-value: 2.73e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 918234684    7 DVACSFRIGSTRSYYqASSNQWHEHpTTWITVKTFRNLATNTRMSIHKGDPVIVTGVLNTEEWV-QDGNKRSRMVVEASS 85
Cdd:TIGR00621  26 NAVANFTLATNRRWK-DQDGEWKEE-TEWHDIVIFGRLAEVAAQYLKKGSLVYVEGRLRTRKWEdQNGQKRSKTEIIADN 103

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 918234684   86 IGhdlsmgysqftrlkSGDPVMAERNARRSVGFVGADSSGKDAGPQSRQQENSDGNQAESLGVDPWNGDE 155
Cdd:TIGR00621 104 VQ--------------LLDLLGARAQGGEFSGGGGSGNRPQGGQEQSATGKDPAQSAPQSGSADPIDGDD 159
 
Name Accession Description Interval E-value
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
10-91 3.52e-21

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 84.12  E-value: 3.52e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 918234684  10 CSFRIGSTRSYYQASsNQWHEhPTTWITVKTFRNLATNTRMSIHKGDPVIVTGVLNTEEWV-QDGNKRSRMVVEASSIGH 88
Cdd:COG0629   26 ANFRLAVNRRYKDQD-GEWKD-ETDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRTRSWEdKDGQKRYTTEVVADEIQF 103


                 ...
gi 918234684  89 DLS 91
Cdd:COG0629  104 LGS 106
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 10-89 1.87e-16

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: 71.49  E-value: 1.87e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 918234684  10 CSFRIGSTRSYYqasSNQWHEHPTTWITVKTFRNLATNTRMSIHKGDPVIVTGVLNTEEWV-QDGNKRSRMVVEASSIGH 88
Cdd:cd04496   23 ARFSLAVNRRRK---DRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRSWEdKDGQKRYGTEVVADRIEF 99


                 .
gi 918234684  89 D 89
Cdd:cd04496  100 L 100
PRK07772 PRK07772
single-stranded DNA-binding protein; Provisional
 10-166 1.14e-13

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236092 [Multi-domain]  Cd Length: 186  Bit Score: 66.21  E-value: 1.14e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 918234684  10 CSFRIGSTRSYYQASSNQWHEHPTTWITVKTFRNLATNTRMSIHKGDPVIVTGVLNTEEW-VQDGNKRSRMVVEASSIGH 88
Cdd:PRK07772  29 ANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIVTGRLKQRSYeTREGEKRTVVELEVDEIGP 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 918234684  89 DLSMGYSQFTRLKSGDpvmaeRNARRSVGFVGA--DSSGKDAGPQSRQQENSDGNQAESLGVDPWNGDEGVGGQNAVTSE 166
Cdd:PRK07772 109 SLRYATAKVTRASRGG-----GGGGGGGGFGGGggGSGGGGGGGGGGGAPGGGGAQASAPADDPWSSAPASGGFGGGDDE 183
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 10-89 1.84e-10

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: 1.84e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 918234684   10 CSFRIGSTRSYyqaSSNQWHEHPTTWITVKTFRNLATNTRMSIHKGDPVIVTGVLNTEEW-VQDGNKRSRMVVEASSIGH 88
Cdd:pfam00436  26 ANFTLATNRRF---KDRGEGDEETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLQTRKYeDQEGQKRYVTEIVADEVQF 102


                  .
gi 918234684   89 D 89
Cdd:pfam00436 103 L 103
PRK05853 PRK05853
hypothetical protein; Validated
 12-129 9.57e-09

hypothetical protein; Validated


Pssm-ID: 235626  Cd Length: 161  Bit Score: 52.53  E-value: 9.57e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 918234684  12 FRIGSTrSYYQASSNQWHEHPTTWITVKTFRNLATNTRMSIHKGDPVIVTGVLNTEEWV-QDGNKRSRMVVEASSIGHDL 90
Cdd:PRK05853  22 FRVASN-SRRRTADGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEYEdRDGNRRSSLEMRATSVGPDL 100

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 918234684  91 SMGYSQFTRLKSGDPVMAERNARRSVGFVGADSSGKDAG 129
Cdd:PRK05853 101 SRCIVRIEKPRYTGPSAGEAPAATGTGAADAADAPASAA 139
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 7-155 2.73e-07

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: 48.18  E-value: 2.73e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 918234684    7 DVACSFRIGSTRSYYqASSNQWHEHpTTWITVKTFRNLATNTRMSIHKGDPVIVTGVLNTEEWV-QDGNKRSRMVVEASS 85
Cdd:TIGR00621  26 NAVANFTLATNRRWK-DQDGEWKEE-TEWHDIVIFGRLAEVAAQYLKKGSLVYVEGRLRTRKWEdQNGQKRSKTEIIADN 103

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 918234684   86 IGhdlsmgysqftrlkSGDPVMAERNARRSVGFVGADSSGKDAGPQSRQQENSDGNQAESLGVDPWNGDE 155
Cdd:TIGR00621 104 VQ--------------LLDLLGARAQGGEFSGGGGSGNRPQGGQEQSATGKDPAQSAPQSGSADPIDGDD 159
PRK08486 PRK08486
single-stranded DNA-binding protein; Provisional
 14-86 6.60e-03

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236275 [Multi-domain]  Cd Length: 182  Bit Score: 35.98  E-value: 6.60e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 918234684  14 IGSTRSYYQASSNQWHEhpTTWITVKTFRNLATNTRMSIHKGDPVIVTGVLNTEEWV-QDGNKRSRMVVEASSI 86
Cdd:PRK08486  31 LATSRRFKKQDGEKGEE--VCFIDIRLFGRTAEIANQYLSKGSKVLIEGRLTFESWMdQNGQKRSKHTITAESM 102
 
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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