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Conserved domains on  [gi|79325179|ref|NP_001031674|]
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plastid transcriptionally active 9 [Arabidopsis thaliana]

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];
99-172 6.69e-06

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


:

Pssm-ID: 440394  Cd Length: 116  Bit Score: 44.83  E-value: 6.69e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79325179  99 NWVNLIGFVDQPVQFEASSDGKFWAG-TVISQRSASDSSG------FWIPIIFEGDLAKTAARYVSKDDQIHVSGKLFID 171
Cdd:COG0629   2 NKVTLVGRLGKDPELRYTPSGTAVANfRLAVNRRYKDQDGewkdetDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRTR 81


                .
gi 79325179 172 S 172
Cdd:COG0629  82 S 82
 
Name Accession Description Interval E-value
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
99-172 6.69e-06

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 44.83  E-value: 6.69e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79325179  99 NWVNLIGFVDQPVQFEASSDGKFWAG-TVISQRSASDSSG------FWIPIIFEGDLAKTAARYVSKDDQIHVSGKLFID 171
Cdd:COG0629   2 NKVTLVGRLGKDPELRYTPSGTAVANfRLAVNRRYKDQDGewkdetDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRTR 81


                .
gi 79325179 172 S 172
Cdd:COG0629  82 S 82
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 101-172 3.27e-05

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: 42.21  E-value: 3.27e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 79325179 101 VNLIGFV-DQPVQFEASSDGKFWAGTVISQRSASDSS-----GFWIPIIFEGDLAKTAARYVSKDDQIHVSGKLFIDS 172
Cdd:cd04496   1 VILIGRLgKDPELRYTPSGTPVARFSLAVNRRRKDRDeeeeeTDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRS 78
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 99-168 5.79e-03

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: 36.06  E-value: 5.79e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 79325179    99 NWVNLIGFV-DQPVQFEASSDGKFWAGTVISQRSASDSSGF-----WIPIIFEGDLAKTAARYVSKDDQIHVSGKL 168
Cdd:pfam00436   2 NKVILVGRLtRDPELRYTPNGNAVANFTLATNRRFKDRGEGdeetdFHRVVVFGKLAEVAAQYLKKGSLVYVEGRL 77
 
Name Accession Description Interval E-value
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
99-172 6.69e-06

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 44.83  E-value: 6.69e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79325179  99 NWVNLIGFVDQPVQFEASSDGKFWAG-TVISQRSASDSSG------FWIPIIFEGDLAKTAARYVSKDDQIHVSGKLFID 171
Cdd:COG0629   2 NKVTLVGRLGKDPELRYTPSGTAVANfRLAVNRRYKDQDGewkdetDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRTR 81


                .
gi 79325179 172 S 172
Cdd:COG0629  82 S 82
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 101-172 3.27e-05

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: 42.21  E-value: 3.27e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 79325179 101 VNLIGFV-DQPVQFEASSDGKFWAGTVISQRSASDSS-----GFWIPIIFEGDLAKTAARYVSKDDQIHVSGKLFIDS 172
Cdd:cd04496   1 VILIGRLgKDPELRYTPSGTPVARFSLAVNRRRKDRDeeeeeTDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRS 78
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 99-168 5.79e-03

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: 36.06  E-value: 5.79e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 79325179    99 NWVNLIGFV-DQPVQFEASSDGKFWAGTVISQRSASDSSGF-----WIPIIFEGDLAKTAARYVSKDDQIHVSGKL 168
Cdd:pfam00436   2 NKVILVGRLtRDPELRYTPNGNAVANFTLATNRRFKDRGEGdeetdFHRVVVFGKLAEVAAQYLKKGSLVYVEGRL 77
 
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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