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Conserved domains on  [gi|78033942|emb|CAJ19941|]
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Single-stranded DNA-binding protein (plasmid) [Xanthomonas euvesicatoria pv. vesicatoria str. 85-10]

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];
12-117 1.43e-21

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


:

Pssm-ID: 440394  Cd Length: 116  Bit Score: 82.19  E-value: 1.43e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942  12 MGFVANEPQLRQ-ANGTPVVNLVVIENEYWKDAEGTRKERSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLRYKPIEGQ 90
Cdd:COG0629   7 VGRLGKDPELRYtPSGTAVANFRLAVNRRYKDQDGEWKDETDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRTRSWEDK 86

                        90       100
                ....*....|....*....|....*....
gi 78033942  91 QYDK--AAEIRGDDFSLLDDPRERDESPD 117
Cdd:COG0629  87 DGQKryTTEVVADEIQFLGSRPSGGGGGD 115
 
Name Accession Description Interval E-value
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
12-117 1.43e-21

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 82.19  E-value: 1.43e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942  12 MGFVANEPQLRQ-ANGTPVVNLVVIENEYWKDAEGTRKERSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLRYKPIEGQ 90
Cdd:COG0629   7 VGRLGKDPELRYtPSGTAVANFRLAVNRRYKDQDGEWKDETDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRTRSWEDK 86

                        90       100
                ....*....|....*....|....*....
gi 78033942  91 QYDK--AAEIRGDDFSLLDDPRERDESPD 117
Cdd:COG0629  87 DGQKryTTEVVADEIQFLGSRPSGGGGGD 115
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 12-106 4.79e-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: 72.64  E-value: 4.79e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942  12 MGFVANEPQLRQ-ANGTPVVNLVVIENEYWKDAEgTRKERSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLRYKPIEGQ 90
Cdd:cd04496   4 IGRLGKDPELRYtPSGTPVARFSLAVNRRRKDRD-EEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRSWEDK 82

                        90
                ....*....|....*...
gi 78033942  91 --QYDKAAEIRGDDFSLL 106
Cdd:cd04496  83 dgQKRYGTEVVADRIEFL 100
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 12-106 1.23e-17

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: 71.88  E-value: 1.23e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942    12 MGFVANEPQLRQ-ANGTPVVNLVVIENEYWKDaEGTRKERSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLRYKPIEGQ 90
Cdd:pfam00436   7 VGRLTRDPELRYtPNGNAVANFTLATNRRFKD-RGEGDEETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLQTRKYEDQ 85

                          90
                  ....*....|....*...
gi 78033942    91 QYDK--AAEIRGDDFSLL 106
Cdd:pfam00436  86 EGQKryVTEIVADEVQFL 103
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 8-107 3.15e-17

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: 72.45  E-value: 3.15e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942     8 RVDCMGFVANEPQLRQA-NGTPVVNLVVIENEYWKDAEGTRKERSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLRYKP 86
Cdd:TIGR00621   6 KVILVGRLTRDPELRYTpSGNAVANFTLATNRRWKDQDGEWKEETEWHDIVIFGRLAEVAAQYLKKGSLVYVEGRLRTRK 85

                          90       100
                  ....*....|....*....|...
gi 78033942    87 IEGQQYDK--AAEIRGDDFSLLD 107
Cdd:TIGR00621  86 WEDQNGQKrsKTEIIADNVQLLD 108
PRK06863 PRK06863
single-stranded DNA-binding protein; Provisional
 8-112 5.54e-11

single-stranded DNA-binding protein; Provisional


Pssm-ID: 136097 [Multi-domain]  Cd Length: 168  Bit Score: 56.13  E-value: 5.54e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942    8 RVDCMGFVANEPQLR-QANGTPVVNLVVIENEYWKDAE-GTRKERSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLRYK 85
Cdd:PRK06863   6 KVIIVGHLGNDPEIRtMPNGEAVANISVATSESWTDKNtGERREVTEWHRIVFYRRQAEVAGEYLRKGSQVYVEGRLKTR 85

                         90       100
                 ....*....|....*....|....*....
gi 78033942   86 PIEGQ--QYDKAAEIRGDDFSLLDDPRER 112
Cdd:PRK06863  86 KWQDQngQDRYTTEIQGDVLQMLGGRNQR 114
 
Name Accession Description Interval E-value
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
12-117 1.43e-21

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 82.19  E-value: 1.43e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942  12 MGFVANEPQLRQ-ANGTPVVNLVVIENEYWKDAEGTRKERSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLRYKPIEGQ 90
Cdd:COG0629   7 VGRLGKDPELRYtPSGTAVANFRLAVNRRYKDQDGEWKDETDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRTRSWEDK 86

                        90       100
                ....*....|....*....|....*....
gi 78033942  91 QYDK--AAEIRGDDFSLLDDPRERDESPD 117
Cdd:COG0629  87 DGQKryTTEVVADEIQFLGSRPSGGGGGD 115
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 12-106 4.79e-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: 72.64  E-value: 4.79e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942  12 MGFVANEPQLRQ-ANGTPVVNLVVIENEYWKDAEgTRKERSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLRYKPIEGQ 90
Cdd:cd04496   4 IGRLGKDPELRYtPSGTPVARFSLAVNRRRKDRD-EEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRSWEDK 82

                        90
                ....*....|....*...
gi 78033942  91 --QYDKAAEIRGDDFSLL 106
Cdd:cd04496  83 dgQKRYGTEVVADRIEFL 100
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 12-106 1.23e-17

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: 71.88  E-value: 1.23e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942    12 MGFVANEPQLRQ-ANGTPVVNLVVIENEYWKDaEGTRKERSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLRYKPIEGQ 90
Cdd:pfam00436   7 VGRLTRDPELRYtPNGNAVANFTLATNRRFKD-RGEGDEETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLQTRKYEDQ 85

                          90
                  ....*....|....*...
gi 78033942    91 QYDK--AAEIRGDDFSLL 106
Cdd:pfam00436  86 EGQKryVTEIVADEVQFL 103
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 8-107 3.15e-17

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: 72.45  E-value: 3.15e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942     8 RVDCMGFVANEPQLRQA-NGTPVVNLVVIENEYWKDAEGTRKERSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLRYKP 86
Cdd:TIGR00621   6 KVILVGRLTRDPELRYTpSGNAVANFTLATNRRWKDQDGEWKEETEWHDIVIFGRLAEVAAQYLKKGSLVYVEGRLRTRK 85

                          90       100
                  ....*....|....*....|...
gi 78033942    87 IEGQQYDK--AAEIRGDDFSLLD 107
Cdd:TIGR00621  86 WEDQNGQKrsKTEIIADNVQLLD 108
PRK06863 PRK06863
single-stranded DNA-binding protein; Provisional
 8-112 5.54e-11

single-stranded DNA-binding protein; Provisional


Pssm-ID: 136097 [Multi-domain]  Cd Length: 168  Bit Score: 56.13  E-value: 5.54e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942    8 RVDCMGFVANEPQLR-QANGTPVVNLVVIENEYWKDAE-GTRKERSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLRYK 85
Cdd:PRK06863   6 KVIIVGHLGNDPEIRtMPNGEAVANISVATSESWTDKNtGERREVTEWHRIVFYRRQAEVAGEYLRKGSQVYVEGRLKTR 85

                         90       100
                 ....*....|....*....|....*....
gi 78033942   86 PIEGQ--QYDKAAEIRGDDFSLLDDPRER 112
Cdd:PRK06863  86 KWQDQngQDRYTTEIQGDVLQMLGGRNQR 114
PRK13732 PRK13732
single-stranded DNA-binding protein; Provisional
 8-88 2.35e-09

single-stranded DNA-binding protein; Provisional


Pssm-ID: 184284 [Multi-domain]  Cd Length: 175  Bit Score: 52.04  E-value: 2.35e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942    8 RVDCMGFVANEPQLRQ-ANGTPVVNLVVIENEYWKDAE-GTRKERSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLRYK 85
Cdd:PRK13732   8 KVILVGRLGKDPEVRYiPNGGAVANLQVATSESWRDKQtGEMREQTEWHRVVLFGKLAEVAGEYLRKGAQVYIEGQLRTR 87


                 ...
gi 78033942   86 PIE 88
Cdd:PRK13732  88 SWE 90
PRK09010 PRK09010
single-stranded DNA-binding protein; Provisional
 8-83 1.04e-08

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236362 [Multi-domain]  Cd Length: 177  Bit Score: 50.23  E-value: 1.04e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 78033942    8 RVDCMGFVANEPQLR-QANGTPVVNLVVIENEYWKD-AEGTRKERSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLR 83
Cdd:PRK09010   8 KVILVGNLGQDPEVRyMPNGGAVANITLATSESWRDkQTGEMKEQTEWHRVVLFGKLAEVAGEYLRKGSQVYIEGQLR 85
PRK05733 PRK05733
single-stranded DNA-binding protein; Provisional
 8-83 1.65e-08

single-stranded DNA-binding protein; Provisional


Pssm-ID: 235585 [Multi-domain]  Cd Length: 172  Bit Score: 49.93  E-value: 1.65e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 78033942    8 RVDCMGFVANEPQLRQ-ANGTPVVNLVVIENEYWKDAE-GTRKERSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLR 83
Cdd:PRK05733   7 KVILVGTCGQDPEVRYlPNGNAVTNLSLATSEQWTDKQsGQKVERTEWHRVSLFGKVAEIAGEYLRKGSQVYIEGKLQ 84
PRK08763 PRK08763
single-stranded DNA-binding protein; Provisional
 8-106 8.06e-08

single-stranded DNA-binding protein; Provisional


Pssm-ID: 181549 [Multi-domain]  Cd Length: 164  Bit Score: 47.63  E-value: 8.06e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942    8 RVDCMGFVANEPQLRQA-NGTPVVNLVVIENEYWKDAEGTRKERSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLRYKP 86
Cdd:PRK08763   7 KVILVGNLGNDPDIKYTqSGMTITRISLATTSVRKDREGNTQERTEWHRVKFFGKLGEIAGEYLRKGSQCYIEGSIRYDK 86

                         90       100
                 ....*....|....*....|..
gi 78033942   87 IEGQ--QYDKAAEIRGDDFSLL 106
Cdd:PRK08763  87 FTGQdgQERYVTEIVADEMQML 108
PRK06958 PRK06958
single-stranded DNA-binding protein; Provisional
 8-106 3.04e-07

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180777 [Multi-domain]  Cd Length: 182  Bit Score: 46.33  E-value: 3.04e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942    8 RVDCMGFVANEPQLR-QANGTPVVNLVVIENEYWKD-AEGTRKERSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLRYK 85
Cdd:PRK06958   6 KVILVGNLGADPEVRyLPSGDAVANIRLATTDRYKDkASGEFKEATEWHRVAFFGRLAEIVGEYLKKGSSVYIEGRIRTR 85

                         90       100
                 ....*....|....*....|...
gi 78033942   86 PIEGQ--QYDKAAEIRGDDFSLL 106
Cdd:PRK06958  86 KWQGQdgQDRYSTEIVADQMQML 108
PRK07274 PRK07274
single-stranded DNA-binding protein; Provisional
 12-112 1.55e-05

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180914  Cd Length: 131  Bit Score: 41.28  E-value: 1.55e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942   12 MGFVANEPQLRQ-ANGTPVVNLVVIENEYWKDAEGTRKerSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLRYKpiegq 90
Cdd:PRK07274   8 IGRLTATPELVKtANDKSVARVTLAVNRRFKNQNGERE--ADFINVVLWGKLAETLASYASKGSLISIDGELRTR----- 80

                         90       100
                 ....*....|....*....|....*...
gi 78033942   91 QYDKAA------EIRGDDFSLLDDPRER 112
Cdd:PRK07274  81 KYEKDGqthyvtEVLCQSFQLLESRAQR 108
PRK06341 PRK06341
single-stranded DNA-binding protein; Provisional
 8-91 6.68e-05

single-stranded DNA-binding protein; Provisional


Pssm-ID: 235782 [Multi-domain]  Cd Length: 166  Bit Score: 39.79  E-value: 6.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942    8 RVDCMGFVANEPQLRQA-NGTPVVNLVVIENEYWKD-AEGTRKERSHAHSIA-FWGPYAETVSKLVQKGSYVRVKGNLRY 84
Cdd:PRK06341   7 KVILIGNLGADPEIRRTqDGRPIANLRIATSETWRDrNSGERKEKTEWHRVViFNEGLCKVAEQYLKKGAKVYIEGQLQT 86


                 ....*..
gi 78033942   85 KPIEGQQ 91
Cdd:PRK06341  87 RKWTDQS 93
PRK06751 PRK06751
single-stranded DNA-binding protein; Provisional
 8-90 6.60e-04

single-stranded DNA-binding protein; Provisional


Pssm-ID: 168659 [Multi-domain]  Cd Length: 173  Bit Score: 37.09  E-value: 6.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78033942    8 RVDCMGFVANEPQLRQA-NGTPVVNLVVIENEYWKDAEGTRKerSHAHSIAFWGPYAETVSKLVQKGSYVRVKGNLRYKP 86
Cdd:PRK06751   4 RVILVGRLTKDPDLRYTpNGVAVATFTLAVNRAFANQQGERE--ADFINCVIWRKQAENVANYLKKGSLAGVDGRLQTRN 81


                 ....
gi 78033942   87 IEGQ 90
Cdd:PRK06751  82 YEGQ 85
 
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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