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Conserved domains on  [gi|1859837974|ref|WP_175337379|]
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single-stranded DNA-binding protein [Leifsonia sp. C5G2]

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];
4-105 2.93e-24

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


:

Pssm-ID: 440394  Cd Length: 116  Bit Score: 89.90  E-value: 2.93e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974   4 TVAVRGFVATEPRHLVTEGGLPITSFRLVTTRRRYNrQAASWEDGgSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLCL 83
Cdd:COG0629     3 KVTLVGRLGKDPELRYTPSGTAVANFRLAVNRRYKD-QDGEWKDE-TDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRT 80

                          90       100
                  ....*....|....*....|....*
gi 1859837974  84 REW---AGEKQgMTVEIEAESIGHD 105
Cdd:COG0629    81 RSWedkDGQKR-YTTEVVADEIQFL 104
 
Name Accession Description Interval E-value
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
4-105 2.93e-24

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 89.90  E-value: 2.93e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974   4 TVAVRGFVATEPRHLVTEGGLPITSFRLVTTRRRYNrQAASWEDGgSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLCL 83
Cdd:COG0629     3 KVTLVGRLGKDPELRYTPSGTAVANFRLAVNRRYKD-QDGEWKDE-TDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRT 80

                          90       100
                  ....*....|....*....|....*
gi 1859837974  84 REW---AGEKQgMTVEIEAESIGHD 105
Cdd:COG0629    81 RSWedkDGQKR-YTTEVVADEIQFL 104
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 5-105 2.79e-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: 84.59  E-value: 2.79e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974   5 VAVRGFVATEPRHLVTEGGLPITSFRLVTTRRRYNRQaasWEDGGSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLCLR 84
Cdd:cd04496     1 VILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDRD---EEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTR 77

                          90       100
                  ....*....|....*....|....
gi 1859837974  85 EW---AGEKQgMTVEIEAESIGHD 105
Cdd:cd04496    78 SWedkDGQKR-YGTEVVADRIEFL 100
PRK07772 PRK07772
single-stranded DNA-binding protein; Provisional
 4-123 3.24e-17

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236092 [Multi-domain]  Cd Length: 186  Bit Score: 73.91  E-value: 3.24e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974   4 TVAVRGFVATEPRHLVTEGGLPITSFRLVTTRRRYNRQAASWEDGGSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLCL 83
Cdd:PRK07772    6 TITVVGNLTADPELRFTPSGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIVTGRLKQ 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1859837974  84 REWA---GEKQgMTVEIEAESIGHDLTWGRSAFTRSPAAAHAG 123
Cdd:PRK07772   86 RSYEtreGEKR-TVVELEVDEIGPSLRYATAKVTRASRGGGGG 127
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 9-105 4.33e-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: 71.11  E-value: 4.33e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974   9 GFVATEPRHLVTEGGLPITSFRLVTTRRRYNRqaaSWEDGGSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLCLREWAG 88
Cdd:pfam00436   8 GRLTRDPELRYTPNGNAVANFTLATNRRFKDR---GEGDEETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLQTRKYED 84

                          90
                  ....*....|....*....
gi 1859837974  89 E--KQGMTVEIEAESIGHD 105
Cdd:pfam00436  85 QegQKRYVTEIVADEVQFL 103
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 20-103 1.60e-12

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: 60.90  E-value: 1.60e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974  20 TEGGLPITSFRLVTTRRRYNRQAaSWEDGgSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLCLREWAgEKQGM---TVE 96
Cdd:TIGR00621  22 TPSGNAVANFTLATNRRWKDQDG-EWKEE-TEWHDIVIFGRLAEVAAQYLKKGSLVYVEGRLRTRKWE-DQNGQkrsKTE 98


                  ....*..
gi 1859837974  97 IEAESIG 103
Cdd:TIGR00621  99 IIADNVQ 105
 
Name Accession Description Interval E-value
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
4-105 2.93e-24

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 89.90  E-value: 2.93e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974   4 TVAVRGFVATEPRHLVTEGGLPITSFRLVTTRRRYNrQAASWEDGgSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLCL 83
Cdd:COG0629     3 KVTLVGRLGKDPELRYTPSGTAVANFRLAVNRRYKD-QDGEWKDE-TDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRT 80

                          90       100
                  ....*....|....*....|....*
gi 1859837974  84 REW---AGEKQgMTVEIEAESIGHD 105
Cdd:COG0629    81 RSWedkDGQKR-YTTEVVADEIQFL 104
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 5-105 2.79e-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: 84.59  E-value: 2.79e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974   5 VAVRGFVATEPRHLVTEGGLPITSFRLVTTRRRYNRQaasWEDGGSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLCLR 84
Cdd:cd04496     1 VILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDRD---EEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTR 77

                          90       100
                  ....*....|....*....|....
gi 1859837974  85 EW---AGEKQgMTVEIEAESIGHD 105
Cdd:cd04496    78 SWedkDGQKR-YGTEVVADRIEFL 100
PRK07772 PRK07772
single-stranded DNA-binding protein; Provisional
 4-123 3.24e-17

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236092 [Multi-domain]  Cd Length: 186  Bit Score: 73.91  E-value: 3.24e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974   4 TVAVRGFVATEPRHLVTEGGLPITSFRLVTTRRRYNRQAASWEDGGSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLCL 83
Cdd:PRK07772    6 TITVVGNLTADPELRFTPSGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIVTGRLKQ 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1859837974  84 REWA---GEKQgMTVEIEAESIGHDLTWGRSAFTRSPAAAHAG 123
Cdd:PRK07772   86 RSYEtreGEKR-TVVELEVDEIGPSLRYATAKVTRASRGGGGG 127
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 9-105 4.33e-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: 71.11  E-value: 4.33e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974   9 GFVATEPRHLVTEGGLPITSFRLVTTRRRYNRqaaSWEDGGSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLCLREWAG 88
Cdd:pfam00436   8 GRLTRDPELRYTPNGNAVANFTLATNRRFKDR---GEGDEETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLQTRKYED 84

                          90
                  ....*....|....*....
gi 1859837974  89 E--KQGMTVEIEAESIGHD 105
Cdd:pfam00436  85 QegQKRYVTEIVADEVQFL 103
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 20-103 1.60e-12

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: 60.90  E-value: 1.60e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974  20 TEGGLPITSFRLVTTRRRYNRQAaSWEDGgSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLCLREWAgEKQGM---TVE 96
Cdd:TIGR00621  22 TPSGNAVANFTLATNRRWKDQDG-EWKEE-TEWHDIVIFGRLAEVAAQYLKKGSLVYVEGRLRTRKWE-DQNGQkrsKTE 98


                  ....*..
gi 1859837974  97 IEAESIG 103
Cdd:TIGR00621  99 IIADNVQ 105
PRK05853 PRK05853
hypothetical protein; Validated
 29-135 1.37e-06

hypothetical protein; Validated


Pssm-ID: 235626  Cd Length: 161  Bit Score: 45.21  E-value: 1.37e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974  29 FRLVTTRRRyNRQAASWEDGGSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLCLREWAgEKQGM---TVEIEAESIGHD 105
Cdd:PRK05853   22 FRVASNSRR-RTADGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEYE-DRDGNrrsSLEMRATSVGPD 99

                          90       100       110
                  ....*....|....*....|....*....|
gi 1859837974 106 LTwgrSAFTRSPAAAHAGEPVDEAATPPEG 135
Cdd:PRK05853  100 LS---RCIVRIEKPRYTGPSAGEAPAATGT 126
PRK05733 PRK05733
single-stranded DNA-binding protein; Provisional
 14-97 6.79e-05

single-stranded DNA-binding protein; Provisional


Pssm-ID: 235585 [Multi-domain]  Cd Length: 172  Bit Score: 40.68  E-value: 6.79e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974  14 EPRHLvtEGGLPITSFRLVTTRRRYNRQAASWEDGgSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLCLREWagEKQGM 93
Cdd:PRK05733   19 EVRYL--PNGNAVTNLSLATSEQWTDKQSGQKVER-TEWHRVSLFGKVAEIAGEYLRKGSQVYIEGKLQTREW--EKDGI 93


                  ....*..
gi 1859837974  94 ---TVEI 97
Cdd:PRK05733   94 kryTTEI 100
PRK08763 PRK08763
single-stranded DNA-binding protein; Provisional
 5-89 9.36e-05

single-stranded DNA-binding protein; Provisional


Pssm-ID: 181549 [Multi-domain]  Cd Length: 164  Bit Score: 40.31  E-value: 9.36e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974   5 VAVRGFVATEPRHLVTEGGLPITSFRLVTTRRRYNRQAASWEDggSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLCLR 84
Cdd:PRK08763    8 VILVGNLGNDPDIKYTQSGMTITRISLATTSVRKDREGNTQER--TEWHRVKFFGKLGEIAGEYLRKGSQCYIEGSIRYD 85


                  ....*
gi 1859837974  85 EWAGE 89
Cdd:PRK08763   86 KFTGQ 90
PRK08182 PRK08182
single-stranded DNA-binding protein; Provisional
 40-135 1.37e-04

single-stranded DNA-binding protein; Provisional


Pssm-ID: 169261  Cd Length: 148  Bit Score: 39.28  E-value: 1.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974  40 RQAASWEDGGSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLCLREW--AGEKQGMTVEIEAESIGhdLTWGR-SAFTRS 116
Cdd:PRK08182   43 TKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVLVEGRMERDEWtdNEDNERVTFKVEARRVG--ILPYRiESVTLS 120

                          90
                  ....*....|....*....
gi 1859837974 117 PAAAHAGEPVDEAATPPEG 135
Cdd:PRK08182  121 PKPAATEPEAEPKPQAAQE 139
PRK13732 PRK13732
single-stranded DNA-binding protein; Provisional
 3-135 1.61e-04

single-stranded DNA-binding protein; Provisional


Pssm-ID: 184284 [Multi-domain]  Cd Length: 175  Bit Score: 39.71  E-value: 1.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974   3 DTVAVRGFVATEPRHLVTEGGLPITSFRLVTTRRRYNRQAASWEDGgSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLC 82
Cdd:PRK13732    7 NKVILVGRLGKDPEVRYIPNGGAVANLQVATSESWRDKQTGEMREQ-TEWHRVVLFGKLAEVAGEYLRKGAQVYIEGQLR 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1859837974  83 LREWagEKQGMT---VEIEAESIGHDLTWGRSAFTRS---PAAAHAGEPVDEAATPPEG 135
Cdd:PRK13732   86 TRSW--EDNGITryvTEILVKTTGTMQMLGRAPQQNAqpqPGPQQNGQPQSADATKKGG 142
PRK06958 PRK06958
single-stranded DNA-binding protein; Provisional
 23-100 2.03e-04

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180777 [Multi-domain]  Cd Length: 182  Bit Score: 39.39  E-value: 2.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859837974  23 GLPITSFRLVTTRRRYNRQAASWEDGgSNWYTVSAFRRLALSAADCIAKGDPVLVSGRLCLREW---AGEKQGMTvEIEA 99
Cdd:PRK06958   25 GDAVANIRLATTDRYKDKASGEFKEA-TEWHRVAFFGRLAEIVGEYLKKGSSVYIEGRIRTRKWqgqDGQDRYST-EIVA 102


                  .
gi 1859837974 100 E 100
Cdd:PRK06958  103 D 103
 
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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