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Conserved domains on  [gi|487918769|ref|WP_001992235|]
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MULTISPECIES: single-stranded DNA-binding protein [Gammaproteobacteria]

Protein Classification

single stranded DNA-binding domain-containing protein( domain architecture ID 489)

single stranded DNA-binding domain-containing protein may bind preferentially to single-stranded DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPA_2b-aaRSs_OBF_like super family cl09930
Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with ...
 1-37 7.20e-09

Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism. This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B, of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases.


The actual alignment was detected with superfamily member TIGR00621:

Pssm-ID: 471953 [Multi-domain]  Cd Length: 164  Bit Score: 47.41  E-value: 7.20e-09
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 487918769    1 MPNVNKVTVMGVLGLNPETKQFSNGGSVTIFSVATTE 37
Cdd:TIGR00621   1 MRMVNKVILVGRLTRDPELRYTPSGNAVANFTLATNR 37
 
Name Accession Description Interval E-value
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 1-37 7.20e-09

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: 47.41  E-value: 7.20e-09
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 487918769    1 MPNVNKVTVMGVLGLNPETKQFSNGGSVTIFSVATTE 37
Cdd:TIGR00621   1 MRMVNKVILVGRLTRDPELRYTPSGNAVANFTLATNR 37
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
4-37 7.09e-08

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 43.67  E-value: 7.09e-08
                         10        20        30
                 ....*....|....*....|....*....|....
gi 487918769   4 VNKVTVMGVLGLNPETKQFSNGGSVTIFSVATTE 37
Cdd:COG0629    1 MNKVTLVGRLGKDPELRYTPSGTAVANFRLAVNR 34
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 4-37 1.16e-06

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: 40.68  E-value: 1.16e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 487918769    4 VNKVTVMGVLGLNPETKQFSNGGSVTIFSVATTE 37
Cdd:pfam00436   1 MNKVILVGRLTRDPELRYTPNGNAVANFTLATNR 34
PRK06863 PRK06863
single-stranded DNA-binding protein; Provisional
 1-37 1.90e-06

single-stranded DNA-binding protein; Provisional


Pssm-ID: 136097 [Multi-domain]  Cd Length: 168  Bit Score: 41.11  E-value: 1.90e-06
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 487918769   1 MPNVNKVTVMGVLGLNPETKQFSNGGSVTIFSVATTE 37
Cdd:PRK06863   1 MAGINKVIIVGHLGNDPEIRTMPNGEAVANISVATSE 37
 
Name Accession Description Interval E-value
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 1-37 7.20e-09

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: 47.41  E-value: 7.20e-09
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 487918769    1 MPNVNKVTVMGVLGLNPETKQFSNGGSVTIFSVATTE 37
Cdd:TIGR00621   1 MRMVNKVILVGRLTRDPELRYTPSGNAVANFTLATNR 37
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
4-37 7.09e-08

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


Pssm-ID: 440394  Cd Length: 116  Bit Score: 43.67  E-value: 7.09e-08
                         10        20        30
                 ....*....|....*....|....*....|....
gi 487918769   4 VNKVTVMGVLGLNPETKQFSNGGSVTIFSVATTE 37
Cdd:COG0629    1 MNKVTLVGRLGKDPELRYTPSGTAVANFRLAVNR 34
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 4-37 1.16e-06

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: 40.68  E-value: 1.16e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 487918769    4 VNKVTVMGVLGLNPETKQFSNGGSVTIFSVATTE 37
Cdd:pfam00436   1 MNKVILVGRLTRDPELRYTPNGNAVANFTLATNR 34
PRK06863 PRK06863
single-stranded DNA-binding protein; Provisional
 1-37 1.90e-06

single-stranded DNA-binding protein; Provisional


Pssm-ID: 136097 [Multi-domain]  Cd Length: 168  Bit Score: 41.11  E-value: 1.90e-06
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 487918769   1 MPNVNKVTVMGVLGLNPETKQFSNGGSVTIFSVATTE 37
Cdd:PRK06863   1 MAGINKVIIVGHLGNDPEIRTMPNGEAVANISVATSE 37
PRK05733 PRK05733
single-stranded DNA-binding protein; Provisional
 4-37 2.79e-06

single-stranded DNA-binding protein; Provisional


Pssm-ID: 235585 [Multi-domain]  Cd Length: 172  Bit Score: 40.68  E-value: 2.79e-06
                         10        20        30
                 ....*....|....*....|....*....|....
gi 487918769   4 VNKVTVMGVLGLNPETKQFSNGGSVTIFSVATTE 37
Cdd:PRK05733   5 VNKVILVGTCGQDPEVRYLPNGNAVTNLSLATSE 38
PRK13732 PRK13732
single-stranded DNA-binding protein; Provisional
 4-37 4.92e-06

single-stranded DNA-binding protein; Provisional


Pssm-ID: 184284 [Multi-domain]  Cd Length: 175  Bit Score: 40.10  E-value: 4.92e-06
                         10        20        30
                 ....*....|....*....|....*....|....
gi 487918769   4 VNKVTVMGVLGLNPETKQFSNGGSVTIFSVATTE 37
Cdd:PRK13732   6 INKVILVGRLGKDPEVRYIPNGGAVANLQVATSE 39
PRK09010 PRK09010
single-stranded DNA-binding protein; Provisional
 4-37 6.25e-06

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236362 [Multi-domain]  Cd Length: 177  Bit Score: 39.44  E-value: 6.25e-06
                         10        20        30
                 ....*....|....*....|....*....|....
gi 487918769   4 VNKVTVMGVLGLNPETKQFSNGGSVTIFSVATTE 37
Cdd:PRK09010   6 VNKVILVGNLGQDPEVRYMPNGGAVANITLATSE 39
PRK06958 PRK06958
single-stranded DNA-binding protein; Provisional
 1-37 1.01e-05

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180777 [Multi-domain]  Cd Length: 182  Bit Score: 39.01  E-value: 1.01e-05
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 487918769   1 MPNVNKVTVMGVLGLNPETKQFSNGGSVTIFSVATTE 37
Cdd:PRK06958   1 MASVNKVILVGNLGADPEVRYLPSGDAVANIRLATTD 37
PRK08763 PRK08763
single-stranded DNA-binding protein; Provisional
 4-36 1.36e-03

single-stranded DNA-binding protein; Provisional


Pssm-ID: 181549 [Multi-domain]  Cd Length: 164  Bit Score: 32.99  E-value: 1.36e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 487918769   4 VNKVTVMGVLGLNPETKQFSNGGSVTIFSVATT 36
Cdd:PRK08763   5 INKVILVGNLGNDPDIKYTQSGMTITRISLATT 37
PRK06642 PRK06642
single-stranded DNA-binding protein; Provisional
 3-37 2.19e-03

single-stranded DNA-binding protein; Provisional


Pssm-ID: 135984  Cd Length: 152  Bit Score: 32.77  E-value: 2.19e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 487918769   3 NVNKVTVMGVLGLNPETKQFSNGGSVTIFSVATTE 37
Cdd:PRK06642   4 SLNKVILIGNVGRDPEIRTTGEGKKIINLSLATTE 38
PRK06341 PRK06341
single-stranded DNA-binding protein; Provisional
 4-37 6.17e-03

single-stranded DNA-binding protein; Provisional


Pssm-ID: 235782 [Multi-domain]  Cd Length: 166  Bit Score: 31.31  E-value: 6.17e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 487918769   4 VNKVTVMGVLGLNPETKQFSNGGSVTIFSVATTE 37
Cdd:PRK06341   5 VNKVILIGNLGADPEIRRTQDGRPIANLRIATSE 38
 
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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