NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|754191270|ref|WP_041806825|]
View 

single-stranded DNA-binding protein [Rhodothermus marinus]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
10-90 3.24e-07

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


:

Pssm-ID: 440394  Cd Length: 116  Bit Score: 45.60  E-value: 3.24e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754191270  10 VNQVILLGRLAEPP--------TPVpdvgeaCQMVLTTEERGRDAAGEPITRLERHlllieepGLTAF------CLQHLQ 75
Cdd:COG0629    1 MNKVTLVGRLGKDPelrytpsgTAV------ANFRLAVNRRYKDQDGEWKDETDWH-------RVVAWgklaenAAEYLK 67

                         90
                 ....*....|....*
gi 754191270  76 VGMTLYVEGSLRRNE 90
Cdd:COG0629   68 KGDKVYVEGRLRTRS 82
 
Name Accession Description Interval E-value
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
10-90 3.24e-07

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 45.60  E-value: 3.24e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754191270  10 VNQVILLGRLAEPP--------TPVpdvgeaCQMVLTTEERGRDAAGEPITRLERHlllieepGLTAF------CLQHLQ 75
Cdd:COG0629    1 MNKVTLVGRLGKDPelrytpsgTAV------ANFRLAVNRRYKDQDGEWKDETDWH-------RVVAWgklaenAAEYLK 67

                         90
                 ....*....|....*
gi 754191270  76 VGMTLYVEGSLRRNE 90
Cdd:COG0629   68 KGDKVYVEGRLRTRS 82
PRK13732 PRK13732
single-stranded DNA-binding protein; Provisional
 5-87 9.08e-06

single-stranded DNA-binding protein; Provisional


Pssm-ID: 184284 [Multi-domain]  Cd Length: 175  Bit Score: 42.41  E-value: 9.08e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754191270   5 MPGRTVNQVILLGRLAEPPTP--VPDVGEACQMVLTTEERGRDA-AGEPITRLERHLLLIEEPgLTAFCLQHLQVGMTLY 81
Cdd:PRK13732   1 MAVRGINKVILVGRLGKDPEVryIPNGGAVANLQVATSESWRDKqTGEMREQTEWHRVVLFGK-LAEVAGEYLRKGAQVY 79


                 ....*.
gi 754191270  82 VEGSLR 87
Cdd:PRK13732  80 IEGQLR 85
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 8-87 3.03e-04

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: 38.17  E-value: 3.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754191270    8 RTVNQVILLGRLAEPP--TPVPDVGEACQMVLTTEERGRDAAGEPITRLERHLLLIEEPgLTAFCLQHLQVGMTLYVEGS 85
Cdd:TIGR00621   2 RMVNKVILVGRLTRDPelRYTPSGNAVANFTLATNRRWKDQDGEWKEETEWHDIVIFGR-LAEVAAQYLKKGSLVYVEGR 80


                  ..
gi 754191270   86 LR 87
Cdd:TIGR00621  81 LR 82
 
Name Accession Description Interval E-value
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
10-90 3.24e-07

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 45.60  E-value: 3.24e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754191270  10 VNQVILLGRLAEPP--------TPVpdvgeaCQMVLTTEERGRDAAGEPITRLERHlllieepGLTAF------CLQHLQ 75
Cdd:COG0629    1 MNKVTLVGRLGKDPelrytpsgTAV------ANFRLAVNRRYKDQDGEWKDETDWH-------RVVAWgklaenAAEYLK 67

                         90
                 ....*....|....*
gi 754191270  76 VGMTLYVEGSLRRNE 90
Cdd:COG0629   68 KGDKVYVEGRLRTRS 82
PRK13732 PRK13732
single-stranded DNA-binding protein; Provisional
 5-87 9.08e-06

single-stranded DNA-binding protein; Provisional


Pssm-ID: 184284 [Multi-domain]  Cd Length: 175  Bit Score: 42.41  E-value: 9.08e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754191270   5 MPGRTVNQVILLGRLAEPPTP--VPDVGEACQMVLTTEERGRDA-AGEPITRLERHLLLIEEPgLTAFCLQHLQVGMTLY 81
Cdd:PRK13732   1 MAVRGINKVILVGRLGKDPEVryIPNGGAVANLQVATSESWRDKqTGEMREQTEWHRVVLFGK-LAEVAGEYLRKGAQVY 79


                 ....*.
gi 754191270  82 VEGSLR 87
Cdd:PRK13732  80 IEGQLR 85
PRK06341 PRK06341
single-stranded DNA-binding protein; Provisional
 5-87 4.60e-05

single-stranded DNA-binding protein; Provisional


Pssm-ID: 235782 [Multi-domain]  Cd Length: 166  Bit Score: 40.56  E-value: 4.60e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754191270   5 MPGrTVNQVILLGRLAEPPT--PVPDVGEACQMVLTTEERGRD-AAGEPITRLERHLLLIEEPGLTAFCLQHLQVGMTLY 81
Cdd:PRK06341   1 MAG-SVNKVILIGNLGADPEirRTQDGRPIANLRIATSETWRDrNSGERKEKTEWHRVVIFNEGLCKVAEQYLKKGAKVY 79


                 ....*.
gi 754191270  82 VEGSLR 87
Cdd:PRK06341  80 IEGQLQ 85
PRK06642 PRK06642
single-stranded DNA-binding protein; Provisional
 5-87 4.79e-05

single-stranded DNA-binding protein; Provisional


Pssm-ID: 135984  Cd Length: 152  Bit Score: 40.47  E-value: 4.79e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754191270   5 MPGrTVNQVILLGRLAEPPTpVPDVGEACQMV---LTTEERGRD-AAGEPITRLERHLLLIEEPGLTAFCLQHLQVGMTL 80
Cdd:PRK06642   1 MAG-SLNKVILIGNVGRDPE-IRTTGEGKKIInlsLATTETWKDrITSERKERTEWHRVVIFSEGLVSVVERYVTKGSKL 78


                 ....*..
gi 754191270  81 YVEGSLR 87
Cdd:PRK06642  79 YIEGSLQ 85
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 8-87 3.03e-04

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: 38.17  E-value: 3.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754191270    8 RTVNQVILLGRLAEPP--TPVPDVGEACQMVLTTEERGRDAAGEPITRLERHLLLIEEPgLTAFCLQHLQVGMTLYVEGS 85
Cdd:TIGR00621   2 RMVNKVILVGRLTRDPelRYTPSGNAVANFTLATNRRWKDQDGEWKEETEWHDIVIFGR-LAEVAAQYLKKGSLVYVEGR 80


                  ..
gi 754191270   86 LR 87
Cdd:TIGR00621  81 LR 82
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH