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Conserved domains on  [gi|2207269276|ref|WP_241211176|]
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MULTISPECIES: single-stranded DNA-binding protein [Acinetobacter]

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];
1-85 3.25e-29

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


:

Pssm-ID: 440394  Cd Length: 116  Bit Score: 100.30  E-value: 3.25e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2207269276   1 MAVNEEWRNDAGDKQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYE-KDGQTVYGTDFIADKVDYLDTKAP 79
Cdd:COG0629    30 LAVNRRYKDQDGEWKDETDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRTRSWEdKDGQKRYTTEVVADEIQFLGSRPS 109


                  ....*.
gi 2207269276  80 GGSNQE 85
Cdd:COG0629   110 GGGGGD 115
 
Name Accession Description Interval E-value
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
1-85 3.25e-29

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 100.30  E-value: 3.25e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2207269276   1 MAVNEEWRNDAGDKQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYE-KDGQTVYGTDFIADKVDYLDTKAP 79
Cdd:COG0629    30 LAVNRRYKDQDGEWKDETDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRTRSWEdKDGQKRYTTEVVADEIQFLGSRPS 109


                  ....*.
gi 2207269276  80 GGSNQE 85
Cdd:COG0629   110 GGGGGD 115
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 1-74 4.28e-22

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: 81.89  E-value: 4.28e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2207269276   1 MAVNEEWRnDAGDKQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYE-KDGQTVYGTDFIADKVDYL 74
Cdd:cd04496    27 LAVNRRRK-DRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRSWEdKDGQKRYGTEVVADRIEFL 100
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 1-85 1.31e-21

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: 82.47  E-value: 1.31e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2207269276   1 MAVNEEWRNDAGDKQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYE-KDGQTVYGTDFIADKVDYLDTKAP 79
Cdd:TIGR00621  33 LATNRRWKDQDGEWKEETEWHDIVIFGRLAEVAAQYLKKGSLVYVEGRLRTRKWEdQNGQKRSKTEIIADNVQLLDLLGA 112


                  ....*.
gi 2207269276  80 GGSNQE 85
Cdd:TIGR00621 113 RAQGGE 118
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 2-74 4.72e-18

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: 71.50  E-value: 4.72e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2207269276   2 AVNEEWRNDaGDKQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYE-KDGQTVYGTDFIADKVDYL 74
Cdd:pfam00436  31 ATNRRFKDR-GEGDEETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLQTRKYEdQEGQKRYVTEIVADEVQFL 103
PRK05733 PRK05733
single-stranded DNA-binding protein; Provisional
 1-69 1.05e-16

single-stranded DNA-binding protein; Provisional


Pssm-ID: 235585 [Multi-domain]  Cd Length: 172  Bit Score: 69.96  E-value: 1.05e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2207269276   1 MAVNEEWRN-DAGDKQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYEKDGQTVYGTDFIAD 69
Cdd:PRK05733   34 LATSEQWTDkQSGQKVERTEWHRVSLFGKVAEIAGEYLRKGSQVYIEGKLQTREWEKDGIKRYTTEIVVD 103
 
Name Accession Description Interval E-value
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
1-85 3.25e-29

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 100.30  E-value: 3.25e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2207269276   1 MAVNEEWRNDAGDKQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYE-KDGQTVYGTDFIADKVDYLDTKAP 79
Cdd:COG0629    30 LAVNRRYKDQDGEWKDETDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRTRSWEdKDGQKRYTTEVVADEIQFLGSRPS 109


                  ....*.
gi 2207269276  80 GGSNQE 85
Cdd:COG0629   110 GGGGGD 115
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 1-74 4.28e-22

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: 81.89  E-value: 4.28e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2207269276   1 MAVNEEWRnDAGDKQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYE-KDGQTVYGTDFIADKVDYL 74
Cdd:cd04496    27 LAVNRRRK-DRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRSWEdKDGQKRYGTEVVADRIEFL 100
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 1-85 1.31e-21

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: 82.47  E-value: 1.31e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2207269276   1 MAVNEEWRNDAGDKQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYE-KDGQTVYGTDFIADKVDYLDTKAP 79
Cdd:TIGR00621  33 LATNRRWKDQDGEWKEETEWHDIVIFGRLAEVAAQYLKKGSLVYVEGRLRTRKWEdQNGQKRSKTEIIADNVQLLDLLGA 112


                  ....*.
gi 2207269276  80 GGSNQE 85
Cdd:TIGR00621 113 RAQGGE 118
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 2-74 4.72e-18

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: 71.50  E-value: 4.72e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2207269276   2 AVNEEWRNDaGDKQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYE-KDGQTVYGTDFIADKVDYL 74
Cdd:pfam00436  31 ATNRRFKDR-GEGDEETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLQTRKYEdQEGQKRYVTEIVADEVQFL 103
PRK05733 PRK05733
single-stranded DNA-binding protein; Provisional
 1-69 1.05e-16

single-stranded DNA-binding protein; Provisional


Pssm-ID: 235585 [Multi-domain]  Cd Length: 172  Bit Score: 69.96  E-value: 1.05e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2207269276   1 MAVNEEWRN-DAGDKQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYEKDGQTVYGTDFIAD 69
Cdd:PRK05733   34 LATSEQWTDkQSGQKVERTEWHRVSLFGKVAEIAGEYLRKGSQVYIEGKLQTREWEKDGIKRYTTEIVVD 103
PRK08763 PRK08763
single-stranded DNA-binding protein; Provisional
 12-81 3.92e-14

single-stranded DNA-binding protein; Provisional


Pssm-ID: 181549 [Multi-domain]  Cd Length: 164  Bit Score: 63.03  E-value: 3.92e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2207269276  12 GDKQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYE-KDGQTVYGTDFIADKVDYLDTKAPGG 81
Cdd:PRK08763   45 GNTQERTEWHRVKFFGKLGEIAGEYLRKGSQCYIEGSIRYDKFTgQDGQERYVTEIVADEMQMLGGRGEGG 115
PRK07274 PRK07274
single-stranded DNA-binding protein; Provisional
 1-78 1.54e-13

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180914  Cd Length: 131  Bit Score: 60.93  E-value: 1.54e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2207269276   1 MAVNEEWRNDAGDKQerTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYEKDGQTVYGTDFIADKVDYLDTKA 78
Cdd:PRK07274   31 LAVNRRFKNQNGERE--ADFINVVLWGKLAETLASYASKGSLISIDGELRTRKYEKDGQTHYVTEVLCQSFQLLESRA 106
PRK13732 PRK13732
single-stranded DNA-binding protein; Provisional
 1-84 1.50e-12

single-stranded DNA-binding protein; Provisional


Pssm-ID: 184284 [Multi-domain]  Cd Length: 175  Bit Score: 59.36  E-value: 1.50e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2207269276   1 MAVNEEWRN-DAGDKQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYEKDGQTVYGTDFIADKVDYLDT--K 77
Cdd:PRK13732   35 VATSESWRDkQTGEMREQTEWHRVVLFGKLAEVAGEYLRKGAQVYIEGQLRTRSWEDNGITRYVTEILVKTTGTMQMlgR 114


                  ....*..
gi 2207269276  78 APGGSNQ 84
Cdd:PRK13732  115 APQQNAQ 121
PRK06863 PRK06863
single-stranded DNA-binding protein; Provisional
 1-77 5.43e-11

single-stranded DNA-binding protein; Provisional


Pssm-ID: 136097 [Multi-domain]  Cd Length: 168  Bit Score: 54.97  E-value: 5.43e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2207269276   1 MAVNEEWRN-DAGDKQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYE-KDGQTVYGTDFIADKVDYLDTK 77
Cdd:PRK06863   33 VATSESWTDkNTGERREVTEWHRIVFYRRQAEVAGEYLRKGSQVYVEGRLKTRKWQdQNGQDRYTTEIQGDVLQMLGGR 111
PRK09010 PRK09010
single-stranded DNA-binding protein; Provisional
 1-67 1.39e-10

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236362 [Multi-domain]  Cd Length: 177  Bit Score: 54.08  E-value: 1.39e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2207269276   1 MAVNEEWRNDA-GDKQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKY-EKDGQTVYGTDFI 67
Cdd:PRK09010   35 LATSESWRDKQtGEMKEQTEWHRVVLFGKLAEVAGEYLRKGSQVYIEGQLRTRKWtDQSGQDRYTTEVV 103
PRK06752 PRK06752
single-stranded DNA-binding protein; Validated
 1-82 1.58e-09

single-stranded DNA-binding protein; Validated


Pssm-ID: 168660  Cd Length: 112  Bit Score: 50.03  E-value: 1.58e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2207269276   1 MAVNEEWRNDAGDKQerTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYEKD-GQTVYGTDFIADKVDYLDTKAP 79
Cdd:PRK06752   31 VAVNRGFRNSLGEQQ--VDFINCVVWRKSAENVTEYCTKGSLVGITGRIHTRNYEDDqGKRIYITEVVIESITFLERRRE 108


                  ...
gi 2207269276  80 GGS 82
Cdd:PRK06752  109 GAS 111
PRK06751 PRK06751
single-stranded DNA-binding protein; Provisional
 1-84 1.73e-09

single-stranded DNA-binding protein; Provisional


Pssm-ID: 168659 [Multi-domain]  Cd Length: 173  Bit Score: 51.34  E-value: 1.73e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2207269276   1 MAVNEEWRNDAGDKQerTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYE-KDGQTVYGTDFIADKVDYLDTKAP 79
Cdd:PRK06751   31 LAVNRAFANQQGERE--ADFINCVIWRKQAENVANYLKKGSLAGVDGRLQTRNYEgQDGKRVYVTEVLAESVQFLEPRNG 108


                  ....*
gi 2207269276  80 GGSNQ 84
Cdd:PRK06751  109 GGEQR 113
PRK07275 PRK07275
single-stranded DNA-binding protein; Provisional
 1-78 6.62e-09

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180915 [Multi-domain]  Cd Length: 162  Bit Score: 49.50  E-value: 6.62e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2207269276   1 MAVNEEWRNDAGDKQerTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKYE-KDGQTVYGTDFIADKVDYLDTKA 78
Cdd:PRK07275   31 LAVNRTFKSQNGERE--ADFINCVIWRQQAENLANWAKKGALIGVTGRIQTRNYEnQQGQRVYVTEVVADNFQMLESRA 107
PRK08486 PRK08486
single-stranded DNA-binding protein; Provisional
 1-50 3.22e-06

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236275 [Multi-domain]  Cd Length: 182  Bit Score: 42.53  E-value: 3.22e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2207269276   1 MAVNEEWRNDAGDKQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIR 50
Cdd:PRK08486   31 LATSRRFKKQDGEKGEEVCFIDIRLFGRTAEIANQYLSKGSKVLIEGRLT 80
PRK07459 PRK07459
single-stranded DNA-binding protein; Provisional
 1-56 6.03e-04

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180986  Cd Length: 121  Bit Score: 35.82  E-value: 6.03e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2207269276   1 MAVNEEWRNDagdkqeRTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKI-------RNTKYEK 56
Cdd:PRK07459   32 LAVNRRSRDD------EPDWFNLEIWGKTAQVAADYVKKGSLIGITGSLkfdrwtdRNTGEDR 88
PRK06341 PRK06341
single-stranded DNA-binding protein; Provisional
 1-81 8.51e-03

single-stranded DNA-binding protein; Provisional


Pssm-ID: 235782 [Multi-domain]  Cd Length: 166  Bit Score: 33.24  E-value: 8.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2207269276   1 MAVNEEWRN-DAGDKQERTDFFRIKCFGSQ-AEAHGKYLGKGSLVFVQGKIRNTKY-EKDGQTVYGTDFIADKVD----Y 73
Cdd:PRK06341   34 IATSETWRDrNSGERKEKTEWHRVVIFNEGlCKVAEQYLKKGAKVYIEGQLQTRKWtDQSGVERYSTEVVLQGFNstltM 113


                  ....*...
gi 2207269276  74 LDTKAPGG 81
Cdd:PRK06341  114 LDGRGEGG 121
PRK06293 PRK06293
single-stranded DNA-binding protein; Provisional
 14-85 9.98e-03

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180517 [Multi-domain]  Cd Length: 161  Bit Score: 32.95  E-value: 9.98e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2207269276  14 KQERTDFFRIKCFGSQAEAHGKYLGKGSLVFVQGKIRNTKY-EKDGQTVYGTDFIADKVDYldtkAPGGSNQE 85
Cdd:PRK06293   38 SKDETVWCRCNIWGNRYDKMLPYLKKGSGVIVAGEMSPESYvDKDGSPQSSLVVSVDTIKF----SPFGRNEG 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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