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Conserved domains on  [gi|489189597|ref|WP_003098976|]
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MULTISPECIES: single-stranded DNA-binding protein [Proteobacteria]

Protein Classification

single-stranded DNA-binding protein( domain architecture ID 10793021)

single-stranded DNA (ssDNA)-binding protein may play a key role in DNA replication, recombination, and repair

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK08182 PRK08182
single-stranded DNA-binding protein; Provisional
 1-144 2.23e-91

single-stranded DNA-binding protein; Provisional


:

Pssm-ID: 169261  Cd Length: 148  Bit Score: 261.54  E-value: 2.23e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189597   1 MSTQFIGEGNIGSPPEYREFPNGNDDPRRLLRLNVYFDNPVPTKGGEFEDRGGFWAPVELWHHDADRWQQLYQKGMRVLV 80
Cdd:PRK08182   1 MSTHFVGEGNIGSAPEYREFPNGNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVLV 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489189597  81 VGRMERDPWTDNEDQPRETWQVNARSVGILPYRIESVALSPKP----QEAEPKPQATQESTAPKETKR 144
Cdd:PRK08182  81 EGRMERDEWTDNEDNERVTFKVEARRVGILPYRIESVTLSPKPaatePEAEPKPQAAQESTAPKEPKR 148
 
Name Accession Description Interval E-value
PRK08182 PRK08182
single-stranded DNA-binding protein; Provisional
 1-144 2.23e-91

single-stranded DNA-binding protein; Provisional


Pssm-ID: 169261  Cd Length: 148  Bit Score: 261.54  E-value: 2.23e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189597   1 MSTQFIGEGNIGSPPEYREFPNGNDDPRRLLRLNVYFDNPVPTKGGEFEDRGGFWAPVELWHHDADRWQQLYQKGMRVLV 80
Cdd:PRK08182   1 MSTHFVGEGNIGSAPEYREFPNGNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVLV 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489189597  81 VGRMERDPWTDNEDQPRETWQVNARSVGILPYRIESVALSPKP----QEAEPKPQATQESTAPKETKR 144
Cdd:PRK08182  81 EGRMERDEWTDNEDNERVTFKVEARRVGILPYRIESVTLSPKPaatePEAEPKPQAAQESTAPKEPKR 148
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 5-110 8.62e-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: 83.43  E-value: 8.62e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189597   5 FIGEGNIGSPPEYREFPNGnddpRRLLRLNVYFDNPVptKGGEFEDRGGFWAPVELWHHDADRWQQLYQKGMRVLVVGRM 84
Cdd:cd04496    1 VILIGRLGKDPELRYTPSG----TPVARFSLAVNRRR--KDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRL 74

                         90       100
                 ....*....|....*....|....*.
gi 489189597  85 ERDPWTDNEDQPRETWQVNARSVGIL 110
Cdd:cd04496   75 RTRSWEDKDGQKRYGTEVVADRIEFL 100
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
3-113 1.92e-21

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 82.96  E-value: 1.92e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189597   3 TQFIGEGNIGSPPEYREFPNGnddpRRLLRLNVYFDNPVPTKGGEFEDRGgFWAPVELWHHDADRWQQLYQKGMRVLVVG 82
Cdd:COG0629    2 NKVTLVGRLGKDPELRYTPSG----TAVANFRLAVNRRYKDQDGEWKDET-DWHRVVAWGKLAENAAEYLKKGDKVYVEG 76

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489189597  83 RMERDPWTDNEDQPRETWQVNARSVGILPYR 113
Cdd:COG0629   77 RLRTRSWEDKDGQKRYTTEVVADEIQFLGSR 107
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 9-110 1.65e-10

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: 54.55  E-value: 1.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189597    9 GNIGSPPEYREFPNGNddprRLLRLNVYFDnpvptkgGEFEDRGGF-----WAPVELWHHDADRWQQLYQKGMRVLVVGR 83
Cdd:pfam00436   8 GRLTRDPELRYTPNGN----AVANFTLATN-------RRFKDRGEGdeetdFHRVVVFGKLAEVAAQYLKKGSLVYVEGR 76

                          90       100
                  ....*....|....*....|....*..
gi 489189597   84 MERDPWTDNEDQPRETWQVNARSVGIL 110
Cdd:pfam00436  77 LQTRKYEDQEGQKRYVTEIVADEVQFL 103
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 9-139 1.00e-07

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: 48.18  E-value: 1.00e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189597    9 GNIGSPPEYREFPNGNDDPRRLLRLNVYFDNpvptKGGEFEDRGGfWAPVELWHHDADRWQQLYQKGMRVLVVGRMERDP 88
Cdd:TIGR00621  11 GRLTRDPELRYTPSGNAVANFTLATNRRWKD----QDGEWKEETE-WHDIVIFGRLAEVAAQYLKKGSLVYVEGRLRTRK 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 489189597   89 WTDNEDQPRETWQVNARSVGILPYRIESVALSPKP--QEAEPKPQATQESTAP 139
Cdd:TIGR00621  86 WEDQNGQKRSKTEIIADNVQLLDLLGARAQGGEFSggGGSGNRPQGGQEQSAT 138
 
Name Accession Description Interval E-value
PRK08182 PRK08182
single-stranded DNA-binding protein; Provisional
 1-144 2.23e-91

single-stranded DNA-binding protein; Provisional


Pssm-ID: 169261  Cd Length: 148  Bit Score: 261.54  E-value: 2.23e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189597   1 MSTQFIGEGNIGSPPEYREFPNGNDDPRRLLRLNVYFDNPVPTKGGEFEDRGGFWAPVELWHHDADRWQQLYQKGMRVLV 80
Cdd:PRK08182   1 MSTHFVGEGNIGSAPEYREFPNGNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVLV 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489189597  81 VGRMERDPWTDNEDQPRETWQVNARSVGILPYRIESVALSPKP----QEAEPKPQATQESTAPKETKR 144
Cdd:PRK08182  81 EGRMERDEWTDNEDNERVTFKVEARRVGILPYRIESVTLSPKPaatePEAEPKPQAAQESTAPKEPKR 148
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 5-110 8.62e-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: 83.43  E-value: 8.62e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189597   5 FIGEGNIGSPPEYREFPNGnddpRRLLRLNVYFDNPVptKGGEFEDRGGFWAPVELWHHDADRWQQLYQKGMRVLVVGRM 84
Cdd:cd04496    1 VILIGRLGKDPELRYTPSG----TPVARFSLAVNRRR--KDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRL 74

                         90       100
                 ....*....|....*....|....*.
gi 489189597  85 ERDPWTDNEDQPRETWQVNARSVGIL 110
Cdd:cd04496   75 RTRSWEDKDGQKRYGTEVVADRIEFL 100
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
3-113 1.92e-21

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 82.96  E-value: 1.92e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189597   3 TQFIGEGNIGSPPEYREFPNGnddpRRLLRLNVYFDNPVPTKGGEFEDRGgFWAPVELWHHDADRWQQLYQKGMRVLVVG 82
Cdd:COG0629    2 NKVTLVGRLGKDPELRYTPSG----TAVANFRLAVNRRYKDQDGEWKDET-DWHRVVAWGKLAENAAEYLKKGDKVYVEG 76

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489189597  83 RMERDPWTDNEDQPRETWQVNARSVGILPYR 113
Cdd:COG0629   77 RLRTRSWEDKDGQKRYTTEVVADEIQFLGSR 107
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 9-110 1.65e-10

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: 54.55  E-value: 1.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189597    9 GNIGSPPEYREFPNGNddprRLLRLNVYFDnpvptkgGEFEDRGGF-----WAPVELWHHDADRWQQLYQKGMRVLVVGR 83
Cdd:pfam00436   8 GRLTRDPELRYTPNGN----AVANFTLATN-------RRFKDRGEGdeetdFHRVVVFGKLAEVAAQYLKKGSLVYVEGR 76

                          90       100
                  ....*....|....*....|....*..
gi 489189597   84 MERDPWTDNEDQPRETWQVNARSVGIL 110
Cdd:pfam00436  77 LQTRKYEDQEGQKRYVTEIVADEVQFL 103
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 9-139 1.00e-07

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: 48.18  E-value: 1.00e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189597    9 GNIGSPPEYREFPNGNDDPRRLLRLNVYFDNpvptKGGEFEDRGGfWAPVELWHHDADRWQQLYQKGMRVLVVGRMERDP 88
Cdd:TIGR00621  11 GRLTRDPELRYTPSGNAVANFTLATNRRWKD----QDGEWKEETE-WHDIVIFGRLAEVAAQYLKKGSLVYVEGRLRTRK 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 489189597   89 WTDNEDQPRETWQVNARSVGILPYRIESVALSPKP--QEAEPKPQATQESTAP 139
Cdd:TIGR00621  86 WEDQNGQKRSKTEIIADNVQLLDLLGARAQGGEFSggGGSGNRPQGGQEQSAT 138
PRK06293 PRK06293
single-stranded DNA-binding protein; Provisional
 9-127 5.13e-04

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180517 [Multi-domain]  Cd Length: 161  Bit Score: 37.96  E-value: 5.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189597   9 GNIGSPPEYREFPNGnddpRRL--LRLNVYFdnpvpTKGGEFEDrggFWAPVELWHHDADRWQQLYQKGMRVLVVGRMER 86
Cdd:PRK06293   8 GRLGADPEERMTSKG----KRVvvLRLGVKS-----RVGSKDET---VWCRCNIWGNRYDKMLPYLKKGSGVIVAGEMSP 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 489189597  87 DPWTDNEDQPRETWQVNARSVGILPYRIESVALSPKPQEAE 127
Cdd:PRK06293  76 ESYVDKDGSPQSSLVVSVDTIKFSPFGRNEGSRQPSAGEDE 116
PRK07772 PRK07772
single-stranded DNA-binding protein; Provisional
 9-108 5.13e-03

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236092 [Multi-domain]  Cd Length: 186  Bit Score: 35.40  E-value: 5.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189597   9 GNIGSPPEYREFPNGN--------DDPRRLLRlnvyfdnpvptKGGEFEDRGGFWAPVELWHHDADRWQQLYQKGMRVLV 80
Cdd:PRK07772  11 GNLTADPELRFTPSGAavanftvaSTPRTFDR-----------QTNEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIV 79

                         90       100
                 ....*....|....*....|....*...
gi 489189597  81 VGRMERDPWTDNEDQPRETWQVNARSVG 108
Cdd:PRK07772  80 TGRLKQRSYETREGEKRTVVELEVDEIG 107
 
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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