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Conserved domains on  [gi|1092593959|ref|WP_070544321|]
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MULTISPECIES: single-stranded DNA-binding protein [Klebsiella]

Protein Classification

single stranded DNA-binding domain-containing protein( domain architecture ID 489)

single stranded DNA-binding domain-containing protein may bind preferentially to single-stranded DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPA_2b-aaRSs_OBF_like super family cl09930
Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with ...
 1-154 1.83e-79

Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism. This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B, of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases.


The actual alignment was detected with superfamily member PRK09010:

Pssm-ID: 471953 [Multi-domain]  Cd Length: 177  Bit Score: 233.97  E-value: 1.83e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   1 MAARGVNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKQTGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYI 80
Cdd:PRK09010    1 MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKQTGEMKEQTEWHRVVLFGKLAEVAGEYLRKGSQVYI 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1092593959  81 EGQLRTRNWQDDAGVTRYVTEVLVGQNGTLQMLGGRRESGEPESAAPQSPATPA--QPaQAPAKSPKAKGGKKGRQ 154
Cdd:PRK09010   81 EGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGQQQGGwgQP-QQPQGGNQFSGGAQSRP 155
 
Name Accession Description Interval E-value
PRK09010 PRK09010
single-stranded DNA-binding protein; Provisional
 1-154 1.83e-79

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236362 [Multi-domain]  Cd Length: 177  Bit Score: 233.97  E-value: 1.83e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   1 MAARGVNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKQTGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYI 80
Cdd:PRK09010    1 MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKQTGEMKEQTEWHRVVLFGKLAEVAGEYLRKGSQVYI 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1092593959  81 EGQLRTRNWQDDAGVTRYVTEVLVGQNGTLQMLGGRRESGEPESAAPQSPATPA--QPaQAPAKSPKAKGGKKGRQ 154
Cdd:PRK09010   81 EGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGQQQGGwgQP-QQPQGGNQFSGGAQSRP 155
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 3-156 1.69e-60

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: 185.31  E-value: 1.69e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   3 ARGVNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKQtGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYIEG 82
Cdd:TIGR00621   1 MRMVNKVILVGRLTRDPELRYTPSGNAVANFTLATNRRWKDQD-GEWKEETEWHDIVIFGRLAEVAAQYLKKGSLVYVEG 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1092593959  83 QLRTRNWQDDAGVTRYVTEVLVGQNGTLQMLGGRRESGEPESAAPQ-SPATPAQPAQAPAKSPKAKGGKKGRQDA 156
Cdd:TIGR00621  80 RLRTRKWEDQNGQKRSKTEIIADNVQLLDLLGARAQGGEFSGGGGSgNRPQGGQEQSATGKDPAQSAPQSGSADP 154
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
6-123 1.26e-54

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 168.48  E-value: 1.26e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   6 VNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDkQTGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQLR 85
Cdd:COG0629     1 MNKVTLVGRLGKDPELRYTPSGTAVANFRLAVNRRYKD-QDGEWKDETDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLR 79

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1092593959  86 TRNWQDDAGVTRYVTEVLVGQngtLQMLGGRRESGEPE 123
Cdd:COG0629    80 TRSWEDKDGQKRYTTEVVADE---IQFLGSRPSGGGGG 114
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 6-113 1.14e-45

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: 145.46  E-value: 1.14e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   6 VNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKQTGEmrENTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQLR 85
Cdd:pfam00436   1 MNKVILVGRLTRDPELRYTPNGNAVANFTLATNRRFKDRGEGD--EETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLQ 78

                          90       100
                  ....*....|....*....|....*...
gi 1092593959  86 TRNWQDDAGVTRYVTEVLVGQngtLQML 113
Cdd:pfam00436  79 TRKYEDQEGQKRYVTEIVADE---VQFL 103
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 9-104 4.67e-40

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: 131.20  E-value: 4.67e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   9 VILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKqtGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQLRTRN 88
Cdd:cd04496     1 VILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDR--DEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRS 78

                          90
                  ....*....|....*.
gi 1092593959  89 WQDDAGVTRYVTEVLV 104
Cdd:cd04496    79 WEDKDGQKRYGTEVVA 94
 
Name Accession Description Interval E-value
PRK09010 PRK09010
single-stranded DNA-binding protein; Provisional
 1-154 1.83e-79

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236362 [Multi-domain]  Cd Length: 177  Bit Score: 233.97  E-value: 1.83e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   1 MAARGVNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKQTGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYI 80
Cdd:PRK09010    1 MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKQTGEMKEQTEWHRVVLFGKLAEVAGEYLRKGSQVYI 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1092593959  81 EGQLRTRNWQDDAGVTRYVTEVLVGQNGTLQMLGGRRESGEPESAAPQSPATPA--QPaQAPAKSPKAKGGKKGRQ 154
Cdd:PRK09010   81 EGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGQQQGGwgQP-QQPQGGNQFSGGAQSRP 155
PRK13732 PRK13732
single-stranded DNA-binding protein; Provisional
 1-156 5.13e-72

single-stranded DNA-binding protein; Provisional


Pssm-ID: 184284 [Multi-domain]  Cd Length: 175  Bit Score: 214.98  E-value: 5.13e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   1 MAARGVNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKQTGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYI 80
Cdd:PRK13732    1 MAVRGINKVILVGRLGKDPEVRYIPNGGAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLAEVAGEYLRKGAQVYI 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1092593959  81 EGQLRTRNWQDDaGVTRYVTEVLVGQNGTLQMLGGRRESGEPESAAPQSPATPaQPAQAPAKSpKAKGGKKGRQDA 156
Cdd:PRK13732   81 EGQLRTRSWEDN-GITRYVTEILVKTTGTMQMLGRAPQQNAQPQPGPQQNGQP-QSADATKKG-GAKTKGRGRKAA 153
PRK05733 PRK05733
single-stranded DNA-binding protein; Provisional
 3-156 1.24e-68

single-stranded DNA-binding protein; Provisional


Pssm-ID: 235585 [Multi-domain]  Cd Length: 172  Bit Score: 206.32  E-value: 1.24e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   3 ARGVNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKQTGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYIEG 82
Cdd:PRK05733    2 ARGVNKVILVGTCGQDPEVRYLPNGNAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAEIAGEYLRKGSQVYIEG 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1092593959  83 QLRTRNWQDDaGVTRYVTEVLVGQNGTLQMLGGR--RESGEPESAAPQSPATPAQPAQAPAKSPKAKGGKKGRQDA 156
Cdd:PRK05733   82 KLQTREWEKD-GIKRYTTEIVVDMQGTMQLLGGRpqGDDQGGQGGGNYNQSAPRQQAQRPQQAAQQQSRPAPQQPA 156
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 3-156 1.69e-60

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: 185.31  E-value: 1.69e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   3 ARGVNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKQtGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYIEG 82
Cdd:TIGR00621   1 MRMVNKVILVGRLTRDPELRYTPSGNAVANFTLATNRRWKDQD-GEWKEETEWHDIVIFGRLAEVAAQYLKKGSLVYVEG 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1092593959  83 QLRTRNWQDDAGVTRYVTEVLVGQNGTLQMLGGRRESGEPESAAPQ-SPATPAQPAQAPAKSPKAKGGKKGRQDA 156
Cdd:TIGR00621  80 RLRTRKWEDQNGQKRSKTEIIADNVQLLDLLGARAQGGEFSGGGGSgNRPQGGQEQSATGKDPAQSAPQSGSADP 154
PRK06863 PRK06863
single-stranded DNA-binding protein; Provisional
 5-146 1.43e-57

single-stranded DNA-binding protein; Provisional


Pssm-ID: 136097 [Multi-domain]  Cd Length: 168  Bit Score: 178.24  E-value: 1.43e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   5 GVNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKQTGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQL 84
Cdd:PRK06863    3 GINKVIIVGHLGNDPEIRTMPNGEAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAEVAGEYLRKGSQVYVEGRL 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1092593959  85 RTRNWQDDAGVTRYVTEVlvgQNGTLQMLGGRRE-----------SGEPESAAPQSPATPAQPAQAPAKSPKA 146
Cdd:PRK06863   83 KTRKWQDQNGQDRYTTEI---QGDVLQMLGGRNQrnaggygnsgpAPQQSYQAGQTNNGNSQQASRPAPQQAA 152
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
6-123 1.26e-54

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 168.48  E-value: 1.26e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   6 VNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDkQTGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQLR 85
Cdd:COG0629     1 MNKVTLVGRLGKDPELRYTPSGTAVANFRLAVNRRYKD-QDGEWKDETDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLR 79

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1092593959  86 TRNWQDDAGVTRYVTEVLVGQngtLQMLGGRRESGEPE 123
Cdd:COG0629    80 TRSWEDKDGQKRYTTEVVADE---IQFLGSRPSGGGGG 114
PRK06958 PRK06958
single-stranded DNA-binding protein; Provisional
 6-120 1.01e-49

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180777 [Multi-domain]  Cd Length: 182  Bit Score: 158.42  E-value: 1.01e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   6 VNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKQTGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQLR 85
Cdd:PRK06958    4 VNKVILVGNLGADPEVRYLPSGDAVANIRLATTDRYKDKASGEFKEATEWHRVAFFGRLAEIVGEYLKKGSSVYIEGRIR 83

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1092593959  86 TRNWQDDAGVTRYVTEVLVGQngtLQMLGGRRESG 120
Cdd:PRK06958   84 TRKWQGQDGQDRYSTEIVADQ---MQMLGGRGGSG 115
PRK06341 PRK06341
single-stranded DNA-binding protein; Provisional
 3-155 1.51e-48

single-stranded DNA-binding protein; Provisional


Pssm-ID: 235782 [Multi-domain]  Cd Length: 166  Bit Score: 154.96  E-value: 1.51e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   3 ARGVNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKQTGEMRENTEWHRVVMFGK-LAEVAGEYLRKGAQVYIE 81
Cdd:PRK06341    2 AGSVNKVILIGNLGADPEIRRTQDGRPIANLRIATSETWRDRNSGERKEKTEWHRVVIFNEgLCKVAEQYLKKGAKVYIE 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1092593959  82 GQLRTRNWQDDAGVTRYVTE-VLVGQNGTLQMLGGRRESGEPESAAPQSPA---TPAQPAQAPAKSPKAKGGKKGRQD 155
Cdd:PRK06341   82 GQLQTRKWTDQSGVERYSTEvVLQGFNSTLTMLDGRGEGGGGGGGGDDGGGgdfGSSGPSRGGPRPASSGGGGNFSRD 159
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 6-113 1.14e-45

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: 145.46  E-value: 1.14e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   6 VNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKQTGEmrENTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQLR 85
Cdd:pfam00436   1 MNKVILVGRLTRDPELRYTPNGNAVANFTLATNRRFKDRGEGD--EETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLQ 78

                          90       100
                  ....*....|....*....|....*...
gi 1092593959  86 TRNWQDDAGVTRYVTEVLVGQngtLQML 113
Cdd:pfam00436  79 TRKYEDQEGQKRYVTEIVADE---VQFL 103
PRK08763 PRK08763
single-stranded DNA-binding protein; Provisional
 3-146 1.35e-42

single-stranded DNA-binding protein; Provisional


Pssm-ID: 181549 [Multi-domain]  Cd Length: 164  Bit Score: 139.69  E-value: 1.35e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   3 ARGVNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKQtGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYIEG 82
Cdd:PRK08763    2 ARGINKVILVGNLGNDPDIKYTQSGMTITRISLATTSVRKDRE-GNTQERTEWHRVKFFGKLGEIAGEYLRKGSQCYIEG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1092593959  83 QLRTRNWQDDAGVTRYVTEVLVGQngtLQMLGGRRESGEPESAA--PQSPATPAQ------PAQAPAKSPKA 146
Cdd:PRK08763   81 SIRYDKFTGQDGQERYVTEIVADE---MQMLGGRGEGGGGGGGGirPQRQPAPRQnngqdyAPRRQQPAPQQ 149
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 9-104 4.67e-40

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: 131.20  E-value: 4.67e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   9 VILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKqtGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQLRTRN 88
Cdd:cd04496     1 VILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDR--DEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRS 78

                          90
                  ....*....|....*.
gi 1092593959  89 WQDDAGVTRYVTEVLV 104
Cdd:cd04496    79 WEDKDGQKRYGTEVVA 94
PRK06642 PRK06642
single-stranded DNA-binding protein; Provisional
 3-129 2.47e-38

single-stranded DNA-binding protein; Provisional


Pssm-ID: 135984  Cd Length: 152  Bit Score: 128.68  E-value: 2.47e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   3 ARGVNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKQTGEMRENTEWHRVVMFGK-LAEVAGEYLRKGAQVYIE 81
Cdd:PRK06642    2 AGSLNKVILIGNVGRDPEIRTTGEGKKIINLSLATTETWKDRITSERKERTEWHRVVIFSEgLVSVVERYVTKGSKLYIE 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1092593959  82 GQLRTRNWQDDAGVTRYVTEVLVgQNGTLQML--------GGRRESGEPESAAPQS 129
Cdd:PRK06642   82 GSLQTRKWNDNSGQEKYTTEVVL-QNFNSQLIlldsknsnNHNQDSGHSEYKHPET 136
PRK08486 PRK08486
single-stranded DNA-binding protein; Provisional
 7-143 2.23e-28

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236275 [Multi-domain]  Cd Length: 182  Bit Score: 104.16  E-value: 2.23e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   7 NKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRdKQTGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQLRT 86
Cdd:PRK08486    3 NKVILVGNLTRDVELRYLPSGSAIATIGLATSRRFK-KQDGEKGEEVCFIDIRLFGRTAEIANQYLSKGSKVLIEGRLTF 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1092593959  87 RNWQDDAGVTRYVTEVLVgqnGTLQMLGGRRESGEPESAAPQS---------PATPAQPAQAPAKS 143
Cdd:PRK08486   82 ESWMDQNGQKRSKHTITA---ESMQMLDSKSDNPQANAMQDNSfhenfnnnyPGNYNNPSQDPYMN 144
PRK07459 PRK07459
single-stranded DNA-binding protein; Provisional
 5-130 4.95e-22

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180986  Cd Length: 121  Bit Score: 85.89  E-value: 4.95e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   5 GVNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKQtgemrenTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQL 84
Cdd:PRK07459    2 SLNSVTLVGRAGRDPEVRYFESGSVVCNLTLAVNRRSRDDE-------PDWFNLEIWGKTAQVAADYVKKGSLIGITGSL 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1092593959  85 RTRNWQD-DAGVTRYVTEVLVGQngtLQMLGGRRESGEPESAAPQSP 130
Cdd:PRK07459   75 KFDRWTDrNTGEDRSKPVIRVDR---LELLGSKRDSEGNANPSNSSE 118
PRK06751 PRK06751
single-stranded DNA-binding protein; Provisional
 6-131 2.03e-20

single-stranded DNA-binding protein; Provisional


Pssm-ID: 168659 [Multi-domain]  Cd Length: 173  Bit Score: 83.31  E-value: 2.03e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   6 VNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDKQtGEmREnTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQLR 85
Cdd:PRK06751    2 MNRVILVGRLTKDPDLRYTPNGVAVATFTLAVNRAFANQQ-GE-RE-ADFINCVIWRKQAENVANYLKKGSLAGVDGRLQ 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1092593959  86 TRNWQDDAGVTRYVTEVLVgqnGTLQMLGGRRESGEPESAAPQSPA 131
Cdd:PRK06751   79 TRNYEGQDGKRVYVTEVLA---ESVQFLEPRNGGGEQRGSFNQQPS 121
PRK07274 PRK07274
single-stranded DNA-binding protein; Provisional
 7-104 1.30e-18

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180914  Cd Length: 131  Bit Score: 77.11  E-value: 1.30e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   7 NKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDkQTGEmREnTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQLRT 86
Cdd:PRK07274    3 NKVILIGRLTATPELVKTANDKSVARVTLAVNRRFKN-QNGE-RE-ADFINVVLWGKLAETLASYASKGSLISIDGELRT 79

                          90
                  ....*....|....*...
gi 1092593959  87 RNWQDDaGVTRYVTEVLV 104
Cdd:PRK07274   80 RKYEKD-GQTHYVTEVLC 96
PRK07275 PRK07275
single-stranded DNA-binding protein; Provisional
 6-143 2.00e-18

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180915 [Multi-domain]  Cd Length: 162  Bit Score: 77.62  E-value: 2.00e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   6 VNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDkQTGEmREnTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQLR 85
Cdd:PRK07275    2 INNVVLVGRMTRDAELRYTPSNVAVATFTLAVNRTFKS-QNGE-RE-ADFINCVIWRQQAENLANWAKKGALIGVTGRIQ 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959  86 TRNWQDDAGVTRYVTEVlVGQNgtLQMLGGR--RESGEPESAAPQSPATPAQPAQAPAKS 143
Cdd:PRK07275   79 TRNYENQQGQRVYVTEV-VADN--FQMLESRatREGGSGGSYNGGFNNAPSANSYSAPAQ 135
PRK06752 PRK06752
single-stranded DNA-binding protein; Validated
 6-118 9.37e-15

single-stranded DNA-binding protein; Validated


Pssm-ID: 168660  Cd Length: 112  Bit Score: 66.60  E-value: 9.37e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   6 VNKVILVGHLGQDPDVRYMPNGGAVASLTLATSETWRDkQTGEmrENTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQLR 85
Cdd:PRK06752    2 MNRVVLIGRLTKEPELYYTKQGVAYARVCVAVNRGFRN-SLGE--QQVDFINCVVWRKSAENVTEYCTKGSLVGITGRIH 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1092593959  86 TRNWQDDAGVTRYVTEVLVgqnGTLQMLGGRRE 118
Cdd:PRK06752   79 TRNYEDDQGKRIYITEVVI---ESITFLERRRE 108
PRK07772 PRK07772
single-stranded DNA-binding protein; Provisional
 11-144 2.79e-13

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236092 [Multi-domain]  Cd Length: 186  Bit Score: 64.67  E-value: 2.79e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959  11 LVGHLGQDPDVRYMPNGGAVASLTLA-TSETWrDKQTGEMRE-NTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQLRTRN 88
Cdd:PRK07772    9 VVGNLTADPELRFTPSGAAVANFTVAsTPRTF-DRQTNEWKDgEALFLRCSIWRQAAENVAESLTKGMRVIVTGRLKQRS 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959  89 WQDDAGVTRYVTEVLV------------------------GQNGTLQMLGGRRESGEPESAAPQSPATPAQPAQAPAKSP 144
Cdd:PRK07772   88 YETREGEKRTVVELEVdeigpslryatakvtrasrgggggGGGGGFGGGGGGSGGGGGGGGGGGAPGGGGAQASAPADDP 167
PRK06293 PRK06293
single-stranded DNA-binding protein; Provisional
 9-104 6.25e-08

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180517 [Multi-domain]  Cd Length: 161  Bit Score: 49.52  E-value: 6.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959   9 VILVGHLGQDPDVRYMPNGGAVASLTLATsetwrdKQTGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQLRTRN 88
Cdd:PRK06293    4 GYIVGRLGADPEERMTSKGKRVVVLRLGV------KSRVGSKDETVWCRCNIWGNRYDKMLPYLKKGSGVIVAGEMSPES 77

                          90
                  ....*....|....*.
gi 1092593959  89 WQDDAGVTRYVTEVLV 104
Cdd:PRK06293   78 YVDKDGSPQSSLVVSV 93
PRK08182 PRK08182
single-stranded DNA-binding protein; Provisional
 13-141 3.19e-04

single-stranded DNA-binding protein; Provisional


Pssm-ID: 169261  Cd Length: 148  Bit Score: 39.28  E-value: 3.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959  13 GHLGQDPDVRYMPNGG----AVASLTLATSETWRDKQTGEMRENTEWHRVVMFGKLAEVAGEYLRKGAQVYIEGQLRTRN 88
Cdd:PRK08182    9 GNIGSAPEYREFPNGNdeprRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVLVEGRMERDE 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092593959  89 WQDDAGVTRYVTEVLVGQNGTLQ------MLGGRRESGEPESAA-PQSPATPAQPAQAPA 141
Cdd:PRK08182   89 WTDNEDNERVTFKVEARRVGILPyriesvTLSPKPAATEPEAEPkPQAAQESTAPKEPKR 148
 
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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