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Conserved domains on  [gi|19115295|ref|NP_594383|]
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single-strand DNA-binding protein Rim1 [Schizosaccharomyces pombe]

Protein Classification

single-stranded DNA-binding protein( domain architecture ID 10450532)

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:  27838363
SCOP:  4000346

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 25-124 2.80e-19

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: 77.28  E-value: 2.80e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115295    25 IQRLTLTGNLTKDVERLQSQKGNEYMRYTVASNN------GKDVAPTFHSVYVFDSyNFDRLQTILRKGTRVYVEADAVW 98
Cdd:pfam00436   1 MNKVILVGRLTRDPELRYTPNGNAVANFTLATNRrfkdrgEGDEETDFHRVVVFGK-LAEVAAQYLKKGSLVYVEGRLQT 79

                          90       100
                  ....*....|....*....|....*.
gi 19115295    99 RSvPAGNEGsQAKMSLRHVSADVLFY 124
Cdd:pfam00436  80 RK-YEDQEG-QKRYVTEIVADEVQFL 103
 
Name Accession Description Interval E-value
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 25-124 2.80e-19

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: 77.28  E-value: 2.80e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115295    25 IQRLTLTGNLTKDVERLQSQKGNEYMRYTVASNN------GKDVAPTFHSVYVFDSyNFDRLQTILRKGTRVYVEADAVW 98
Cdd:pfam00436   1 MNKVILVGRLTRDPELRYTPNGNAVANFTLATNRrfkdrgEGDEETDFHRVVVFGK-LAEVAAQYLKKGSLVYVEGRLQT 79

                          90       100
                  ....*....|....*....|....*.
gi 19115295    99 RSvPAGNEGsQAKMSLRHVSADVLFY 124
Cdd:pfam00436  80 RK-YEDQEG-QKRYVTEIVADEVQFL 103
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 29-123 7.36e-14

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: 63.01  E-value: 7.36e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115295  29 TLTGNLTKDVERLQSQKGNEYMRYTVASNNG------KDVAPTFHSVYVFDSyNFDRLQTILRKGTRVYVEADAVWRSVP 102
Cdd:cd04496   2 ILIGRLGKDPELRYTPSGTPVARFSLAVNRRrkdrdeEEEETDWIRVVAFGK-LAENAAKYLKKGDLVYVEGRLRTRSWE 80

                        90       100
                ....*....|....*....|.
gi 19115295 103 agNEGSQAKMSLRHVSADVLF 123
Cdd:cd04496  81 --DKDGQKRYGTEVVADRIEF 99
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
27-93 4.94e-08

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 48.30  E-value: 4.94e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19115295  27 RLTLTGNLTKDVERLQSQKGNEYMRYTVASN------NGKDVAPT-FHSVYVFDSyNFDRLQTILRKGTRVYVE 93
Cdd:COG0629   3 KVTLVGRLGKDPELRYTPSGTAVANFRLAVNrrykdqDGEWKDETdWHRVVAWGK-LAENAAEYLKKGDKVYVE 75
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 23-93 4.85e-05

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: 41.25  E-value: 4.85e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115295    23 RDIQRLTLTGNLTKDVERLQSQKGNEYMRYTVASN--------NGKDVApTFHSVYVF-----DSYNFdrlqtiLRKGTR 89
Cdd:TIGR00621   2 RMVNKVILVGRLTRDPELRYTPSGNAVANFTLATNrrwkdqdgEWKEET-EWHDIVIFgrlaeVAAQY------LKKGSL 74


                  ....
gi 19115295    90 VYVE 93
Cdd:TIGR00621  75 VYVE 78
 
Name Accession Description Interval E-value
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 25-124 2.80e-19

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: 77.28  E-value: 2.80e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115295    25 IQRLTLTGNLTKDVERLQSQKGNEYMRYTVASNN------GKDVAPTFHSVYVFDSyNFDRLQTILRKGTRVYVEADAVW 98
Cdd:pfam00436   1 MNKVILVGRLTRDPELRYTPNGNAVANFTLATNRrfkdrgEGDEETDFHRVVVFGK-LAEVAAQYLKKGSLVYVEGRLQT 79

                          90       100
                  ....*....|....*....|....*.
gi 19115295    99 RSvPAGNEGsQAKMSLRHVSADVLFY 124
Cdd:pfam00436  80 RK-YEDQEG-QKRYVTEIVADEVQFL 103
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 29-123 7.36e-14

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: 63.01  E-value: 7.36e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115295  29 TLTGNLTKDVERLQSQKGNEYMRYTVASNNG------KDVAPTFHSVYVFDSyNFDRLQTILRKGTRVYVEADAVWRSVP 102
Cdd:cd04496   2 ILIGRLGKDPELRYTPSGTPVARFSLAVNRRrkdrdeEEEETDWIRVVAFGK-LAENAAKYLKKGDLVYVEGRLRTRSWE 80

                        90       100
                ....*....|....*....|.
gi 19115295 103 agNEGSQAKMSLRHVSADVLF 123
Cdd:cd04496  81 --DKDGQKRYGTEVVADRIEF 99
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
27-93 4.94e-08

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 48.30  E-value: 4.94e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19115295  27 RLTLTGNLTKDVERLQSQKGNEYMRYTVASN------NGKDVAPT-FHSVYVFDSyNFDRLQTILRKGTRVYVE 93
Cdd:COG0629   3 KVTLVGRLGKDPELRYTPSGTAVANFRLAVNrrykdqDGEWKDETdWHRVVAWGK-LAENAAEYLKKGDKVYVE 75
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 23-93 4.85e-05

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: 41.25  E-value: 4.85e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115295    23 RDIQRLTLTGNLTKDVERLQSQKGNEYMRYTVASN--------NGKDVApTFHSVYVF-----DSYNFdrlqtiLRKGTR 89
Cdd:TIGR00621   2 RMVNKVILVGRLTRDPELRYTPSGNAVANFTLATNrrwkdqdgEWKEET-EWHDIVIFgrlaeVAAQY------LKKGSL 74


                  ....
gi 19115295    90 VYVE 93
Cdd:TIGR00621  75 VYVE 78
 
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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