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Conserved domains on  [gi|495172054|ref|WP_007896849|]
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MULTISPECIES: single-stranded DNA-binding protein [Bacteroidales]

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 ...
 10-106 1.78e-18

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: 74.19  E-value: 1.78e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495172054  10 VTGFIGKDAEIHQFTS-ASVARFSLAVSRLEKNGEESNRISAFMNIEAWRKN-ENTDSFdmLTKGTMLTVEGYFKPEEWI 87
Cdd:cd04496    3 LIGRLGKDPELRYTPSgTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLaENAAKY--LKKGDLVYVEGRLRTRSWE 80

                         90
                 ....*....|....*....
gi 495172054  88 DKDGTKHNRIVTVAVKFYP 106
Cdd:cd04496   81 DKDGQKRYGTEVVADRIEF 99
 
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 ...
 10-106 1.78e-18

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: 74.19  E-value: 1.78e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495172054  10 VTGFIGKDAEIHQFTS-ASVARFSLAVSRLEKNGEESNRISAFMNIEAWRKN-ENTDSFdmLTKGTMLTVEGYFKPEEWI 87
Cdd:cd04496    3 LIGRLGKDPELRYTPSgTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLaENAAKY--LKKGDLVYVEGRLRTRSWE 80

                         90
                 ....*....|....*....
gi 495172054  88 DKDGTKHNRIVTVAVKFYP 106
Cdd:cd04496   81 DKDGQKRYGTEVVADRIEF 99
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
6-106 4.72e-18

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 73.72  E-value: 4.72e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495172054   6 NTFAVTGFIGKDAEIHQFTS-ASVARFSLAVSRLEKN--GEESNRiSAFMNIEAWRKN-ENTDSFdmLTKGTMLTVEGYF 81
Cdd:COG0629    2 NKVTLVGRLGKDPELRYTPSgTAVANFRLAVNRRYKDqdGEWKDE-TDWHRVVAWGKLaENAAEY--LKKGDKVYVEGRL 78

                         90       100
                 ....*....|....*....|....*
gi 495172054  82 KPEEWIDKDGTKHNRIVTVAVKFYP 106
Cdd:COG0629   79 RTRSWEDKDGQKRYTTEVVADEIQF 103
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 6-105 4.85e-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: 63.02  E-value: 4.85e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495172054    6 NTFAVTGFIGKDAEIHQFTS-ASVARFSLAVSRLEKNGEESNRISAFMNIEAWRKNENTDSfDMLTKGTMLTVEGYFKPE 84
Cdd:pfam00436   2 NKVILVGRLTRDPELRYTPNgNAVANFTLATNRRFKDRGEGDEETDFHRVVVFGKLAEVAA-QYLKKGSLVYVEGRLQTR 80

                          90       100
                  ....*....|....*....|...
gi 495172054   85 EWIDKDGTKHNR--IVTVAVKFY 105
Cdd:pfam00436  81 KYEDQEGQKRYVteIVADEVQFL 103
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 6-104 8.16e-11

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: 55.89  E-value: 8.16e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495172054    6 NTFAVTGFIGKDAEIHQFTS-ASVARFSLAVSRL--EKNGEESNRiSAFMNIEAWRK-NENTDSFdmLTKGTMLTVEGYF 81
Cdd:TIGR00621   5 NKVILVGRLTRDPELRYTPSgNAVANFTLATNRRwkDQDGEWKEE-TEWHDIVIFGRlAEVAAQY--LKKGSLVYVEGRL 81

                          90       100
                  ....*....|....*....|...
gi 495172054   82 KPEEWIDKDGTKHNRIVTVAVKF 104
Cdd:TIGR00621  82 RTRKWEDQNGQKRSKTEIIADNV 104
PRK07459 PRK07459
single-stranded DNA-binding protein; Provisional
 6-96 1.55e-08

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180986  Cd Length: 121  Bit Score: 49.30  E-value: 1.55e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495172054   6 NTFAVTGFIGKDAEIHQFTSASV-ARFSLAVSRLEKNGEESnrisaFMNIEAWRKNENTDSfDMLTKGTMLTVEGYFKPE 84
Cdd:PRK07459   4 NSVTLVGRAGRDPEVRYFESGSVvCNLTLAVNRRSRDDEPD-----WFNLEIWGKTAQVAA-DYVKKGSLIGITGSLKFD 77

                         90
                 ....*....|..
gi 495172054  85 EWIDKDgTKHNR 96
Cdd:PRK07459  78 RWTDRN-TGEDR 88
 
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 ...
 10-106 1.78e-18

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: 74.19  E-value: 1.78e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495172054  10 VTGFIGKDAEIHQFTS-ASVARFSLAVSRLEKNGEESNRISAFMNIEAWRKN-ENTDSFdmLTKGTMLTVEGYFKPEEWI 87
Cdd:cd04496    3 LIGRLGKDPELRYTPSgTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLaENAAKY--LKKGDLVYVEGRLRTRSWE 80

                         90
                 ....*....|....*....
gi 495172054  88 DKDGTKHNRIVTVAVKFYP 106
Cdd:cd04496   81 DKDGQKRYGTEVVADRIEF 99
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
6-106 4.72e-18

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 73.72  E-value: 4.72e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495172054   6 NTFAVTGFIGKDAEIHQFTS-ASVARFSLAVSRLEKN--GEESNRiSAFMNIEAWRKN-ENTDSFdmLTKGTMLTVEGYF 81
Cdd:COG0629    2 NKVTLVGRLGKDPELRYTPSgTAVANFRLAVNRRYKDqdGEWKDE-TDWHRVVAWGKLaENAAEY--LKKGDKVYVEGRL 78

                         90       100
                 ....*....|....*....|....*
gi 495172054  82 KPEEWIDKDGTKHNRIVTVAVKFYP 106
Cdd:COG0629   79 RTRSWEDKDGQKRYTTEVVADEIQF 103
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 6-105 4.85e-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: 63.02  E-value: 4.85e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495172054    6 NTFAVTGFIGKDAEIHQFTS-ASVARFSLAVSRLEKNGEESNRISAFMNIEAWRKNENTDSfDMLTKGTMLTVEGYFKPE 84
Cdd:pfam00436   2 NKVILVGRLTRDPELRYTPNgNAVANFTLATNRRFKDRGEGDEETDFHRVVVFGKLAEVAA-QYLKKGSLVYVEGRLQTR 80

                          90       100
                  ....*....|....*....|...
gi 495172054   85 EWIDKDGTKHNR--IVTVAVKFY 105
Cdd:pfam00436  81 KYEDQEGQKRYVteIVADEVQFL 103
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 6-104 8.16e-11

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: 55.89  E-value: 8.16e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495172054    6 NTFAVTGFIGKDAEIHQFTS-ASVARFSLAVSRL--EKNGEESNRiSAFMNIEAWRK-NENTDSFdmLTKGTMLTVEGYF 81
Cdd:TIGR00621   5 NKVILVGRLTRDPELRYTPSgNAVANFTLATNRRwkDQDGEWKEE-TEWHDIVIFGRlAEVAAQY--LKKGSLVYVEGRL 81

                          90       100
                  ....*....|....*....|...
gi 495172054   82 KPEEWIDKDGTKHNRIVTVAVKF 104
Cdd:TIGR00621  82 RTRKWEDQNGQKRSKTEIIADNV 104
PRK07459 PRK07459
single-stranded DNA-binding protein; Provisional
 6-96 1.55e-08

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180986  Cd Length: 121  Bit Score: 49.30  E-value: 1.55e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495172054   6 NTFAVTGFIGKDAEIHQFTSASV-ARFSLAVSRLEKNGEESnrisaFMNIEAWRKNENTDSfDMLTKGTMLTVEGYFKPE 84
Cdd:PRK07459   4 NSVTLVGRAGRDPEVRYFESGSVvCNLTLAVNRRSRDDEPD-----WFNLEIWGKTAQVAA-DYVKKGSLIGITGSLKFD 77

                         90
                 ....*....|..
gi 495172054  85 EWIDKDgTKHNR 96
Cdd:PRK07459  78 RWTDRN-TGEDR 88
PRK07274 PRK07274
single-stranded DNA-binding protein; Provisional
 19-94 8.27e-05

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180914  Cd Length: 131  Bit Score: 39.36  E-value: 8.27e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 495172054  19 EIHQFTS-ASVARFSLAVSRLEKNgEESNRISAFMNIEAW-RKNENTDSFDmlTKGTMLTVEGYFKPEEWiDKDGTKH 94
Cdd:PRK07274  16 ELVKTANdKSVARVTLAVNRRFKN-QNGEREADFINVVLWgKLAETLASYA--SKGSLISIDGELRTRKY-EKDGQTH 89
PRK06863 PRK06863
single-stranded DNA-binding protein; Provisional
 6-91 7.10e-04

single-stranded DNA-binding protein; Provisional


Pssm-ID: 136097 [Multi-domain]  Cd Length: 168  Bit Score: 37.25  E-value: 7.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495172054   6 NTFAVTGFIGKDAEIHQFTSA-SVARFSLAVSR--LEKNGEESNRISAFMNIEAWRKNENTDSfDMLTKGTMLTVEGYFK 82
Cdd:PRK06863   5 NKVIIVGHLGNDPEIRTMPNGeAVANISVATSEswTDKNTGERREVTEWHRIVFYRRQAEVAG-EYLRKGSQVYVEGRLK 83


                 ....*....
gi 495172054  83 PEEWIDKDG 91
Cdd:PRK06863  84 TRKWQDQNG 92
PRK06293 PRK06293
single-stranded DNA-binding protein; Provisional
 12-112 1.64e-03

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180517 [Multi-domain]  Cd Length: 161  Bit Score: 36.42  E-value: 1.64e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495172054  12 GFIGKDAEIhQFTSAS--VARFSLAVSrlEKNGEESNRIsafmnieAWRKNENTDSFD----MLTKGTMLTVEGYFKPEE 85
Cdd:PRK06293   8 GRLGADPEE-RMTSKGkrVVVLRLGVK--SRVGSKDETV-------WCRCNIWGNRYDkmlpYLKKGSGVIVAGEMSPES 77

                         90       100
                 ....*....|....*....|....*....
gi 495172054  86 WIDKDGTKHNRIVTVA--VKFYPPVEKEE 112
Cdd:PRK06293  78 YVDKDGSPQSSLVVSVdtIKFSPFGRNEG 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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