NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|489515573|ref|WP_003420408|]
View 

MULTISPECIES: YbaB/EbfC family nucleoid-associated protein [Mycobacterium]

Protein Classification

YbaB/EbfC family nucleoid-associated protein( domain architecture ID 10002284)

YbaB/EbfC family nucleoid-associated protein is a DNA-binding protein that may be involved in DNA repair

CATH:  3.30.1310.10
Gene Ontology:  GO:0003677
PubMed:  36296221|19594923
SCOP:  4003186

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
YbaB COG0718
DNA-binding nucleoid-associated protein YbaB/EfbC [Transcription];
23-96 6.07e-26

DNA-binding nucleoid-associated protein YbaB/EfbC [Transcription];


:

Pssm-ID: 440482  Cd Length: 100  Bit Score: 93.65  E-value: 6.07e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489515573  23 EAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDPDDIETLQDLIVGAMRDASQQVTKMAQERLGAL 96
Cdd:COG0718   18 EAQEELAELEVEGESGGGLVKVTVNGKGEVKSIEIDPSLLDPEDKEMLEDLIVAAVNDALRKAEELAQEEMGKL 91
 
Name Accession Description Interval E-value
YbaB COG0718
DNA-binding nucleoid-associated protein YbaB/EfbC [Transcription];
23-96 6.07e-26

DNA-binding nucleoid-associated protein YbaB/EfbC [Transcription];


Pssm-ID: 440482  Cd Length: 100  Bit Score: 93.65  E-value: 6.07e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489515573  23 EAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDPDDIETLQDLIVGAMRDASQQVTKMAQERLGAL 96
Cdd:COG0718   18 EAQEELAELEVEGESGGGLVKVTVNGKGEVKSIEIDPSLLDPEDKEMLEDLIVAAVNDALRKAEELAQEEMGKL 91
YbaB_DNA_bd pfam02575
YbaB/EbfC DNA-binding family; This is a family of DNA-binding proteins. Members of this family ...
 23-96 7.49e-26

YbaB/EbfC DNA-binding family; This is a family of DNA-binding proteins. Members of this family form homodimers which bind DNA via a tweezer-like structure. The conformation of the DNA is changed when bound to these proteins. In bacteria, these proteins may play a role in DNA replication-recovery following DNA damage.


Pssm-ID: 460599  Cd Length: 90  Bit Score: 92.92  E-value: 7.49e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489515573   23 EAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDPDDIETLQDLIVGAMRDASQQVTKMAQERLGAL 96
Cdd:pfam02575  12 EAQEELAEKEVEGTSGGGLVKVTVNGKGEVKSIEIDPELVDPEDVEMLEDLIVAAVNDALRKAEELAEEEMGKL 85
DNA_YbaB_EbfC TIGR00103
DNA-binding protein, YbaB/EbfC family; The function of this protein is unknown, but it has ...
 16-86 4.41e-09

DNA-binding protein, YbaB/EbfC family; The function of this protein is unknown, but it has been expressed and crystallized. Its gene nearly always occurs next to recR and/or dnaX. It is restricted to Bacteria and the plant Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A member is present even in the minimal gene complement of Mycoplasm genitalium. [Unknown function, General]


Pssm-ID: 211546  Cd Length: 101  Bit Score: 50.51  E-value: 4.41e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489515573   16 QMQQKLLEAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDpDDIETLQDLIVGAMRDASQQVT 86
Cdd:TIGR00103  15 QMQEKMKKLQEEIAQFEVTGKSGAGLVKVTINGNLELKSIEIDPSLLE-EDKEALEDMITEALNDAVKKVE 84
PRK14625 PRK14625
hypothetical protein; Provisional
 6-85 2.43e-08

hypothetical protein; Provisional


Pssm-ID: 184772  Cd Length: 109  Bit Score: 48.77  E-value: 2.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489515573   6 DMSALLAQAQQMQQKLLEAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDPDDIETLQDLIVGAMRDASQQV 85
Cdd:PRK14625   3 DLGGLMKQAQAMQQKLADAQARLAETTVEGTSGGGMVTVTLMGNGELVRVLMDESLVQPGEGEVIADLIVAAHADAKKKL 82
 
Name Accession Description Interval E-value
YbaB COG0718
DNA-binding nucleoid-associated protein YbaB/EfbC [Transcription];
23-96 6.07e-26

DNA-binding nucleoid-associated protein YbaB/EfbC [Transcription];


Pssm-ID: 440482  Cd Length: 100  Bit Score: 93.65  E-value: 6.07e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489515573  23 EAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDPDDIETLQDLIVGAMRDASQQVTKMAQERLGAL 96
Cdd:COG0718   18 EAQEELAELEVEGESGGGLVKVTVNGKGEVKSIEIDPSLLDPEDKEMLEDLIVAAVNDALRKAEELAQEEMGKL 91
YbaB_DNA_bd pfam02575
YbaB/EbfC DNA-binding family; This is a family of DNA-binding proteins. Members of this family ...
 23-96 7.49e-26

YbaB/EbfC DNA-binding family; This is a family of DNA-binding proteins. Members of this family form homodimers which bind DNA via a tweezer-like structure. The conformation of the DNA is changed when bound to these proteins. In bacteria, these proteins may play a role in DNA replication-recovery following DNA damage.


Pssm-ID: 460599  Cd Length: 90  Bit Score: 92.92  E-value: 7.49e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489515573   23 EAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDPDDIETLQDLIVGAMRDASQQVTKMAQERLGAL 96
Cdd:pfam02575  12 EAQEELAEKEVEGTSGGGLVKVTVNGKGEVKSIEIDPELVDPEDVEMLEDLIVAAVNDALRKAEELAEEEMGKL 85
DNA_YbaB_EbfC TIGR00103
DNA-binding protein, YbaB/EbfC family; The function of this protein is unknown, but it has ...
 16-86 4.41e-09

DNA-binding protein, YbaB/EbfC family; The function of this protein is unknown, but it has been expressed and crystallized. Its gene nearly always occurs next to recR and/or dnaX. It is restricted to Bacteria and the plant Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A member is present even in the minimal gene complement of Mycoplasm genitalium. [Unknown function, General]


Pssm-ID: 211546  Cd Length: 101  Bit Score: 50.51  E-value: 4.41e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489515573   16 QMQQKLLEAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDpDDIETLQDLIVGAMRDASQQVT 86
Cdd:TIGR00103  15 QMQEKMKKLQEEIAQFEVTGKSGAGLVKVTINGNLELKSIEIDPSLLE-EDKEALEDMITEALNDAVKKVE 84
PRK14625 PRK14625
hypothetical protein; Provisional
 6-85 2.43e-08

hypothetical protein; Provisional


Pssm-ID: 184772  Cd Length: 109  Bit Score: 48.77  E-value: 2.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489515573   6 DMSALLAQAQQMQQKLLEAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDPDDIETLQDLIVGAMRDASQQV 85
Cdd:PRK14625   3 DLGGLMKQAQAMQQKLADAQARLAETTVEGTSGGGMVTVTLMGNGELVRVLMDESLVQPGEGEVIADLIVAAHADAKKKL 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