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Conserved domains on  [gi|145298|gb|AAA23458|]
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orf12 ORF [Escherichia coli]

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:  19594923|19208644
SCOP:  4003186

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YbaB COG0718
DNA-binding nucleoid-associated protein YbaB/EfbC [Transcription];
6-102 3.50e-43

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


:

Pssm-ID: 440482  Cd Length: 100  Bit Score: 136.03  E-value: 3.50e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145298     6 GLGNLMKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE-DDKEMLEDLVAAAFNDAARRI 84
Cdd:COG0718   1 NMGGLMKQAQKMQEKMQEAQEELAELEVEGESGGGLVKVTVNGKGEVKSIEIDPSLLDpEDKEMLEDLIVAAVNDALRKA 80

                        90
                ....*....|....*...
gi 145298    85 EETQKEKMASVSSGMQLP 102
Cdd:COG0718  81 EELAQEEMGKLTGGLNLP 98
 
Name Accession Description Interval E-value
YbaB COG0718
DNA-binding nucleoid-associated protein YbaB/EfbC [Transcription];
6-102 3.50e-43

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


Pssm-ID: 440482  Cd Length: 100  Bit Score: 136.03  E-value: 3.50e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145298     6 GLGNLMKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE-DDKEMLEDLVAAAFNDAARRI 84
Cdd:COG0718   1 NMGGLMKQAQKMQEKMQEAQEELAELEVEGESGGGLVKVTVNGKGEVKSIEIDPSLLDpEDKEMLEDLIVAAVNDALRKA 80

                        90
                ....*....|....*...
gi 145298    85 EETQKEKMASVSSGMQLP 102
Cdd:COG0718  81 EELAQEEMGKLTGGLNLP 98
DNA_YbaB_EbfC TIGR00103
DNA-binding protein, YbaB/EbfC family; The function of this protein is unknown, but it has ...
 1-105 1.33e-40

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: 129.86  E-value: 1.33e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145298       1 MFGKGgLGNLMKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLEDDKEMLEDLVAAAFNDA 80
Cdd:TIGR00103   1 SFGKN-LGELMKQAQQMQEKMKKLQEEIAQFEVTGKSGAGLVKVTINGNLELKSIEIDPSLLEEDKEALEDMITEALNDA 79

                          90       100
                  ....*....|....*....|....*
gi 145298      81 ARRIEETQKEKMasvSSGMQLPPGF 105
Cdd:TIGR00103  80 VKKVEETYKELM---TSGMPLPPGL 101
YbaB_DNA_bd pfam02575
YbaB/EbfC DNA-binding family; This is a family of DNA-binding proteins. Members of this family ...
 12-100 1.58e-37

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: 121.42  E-value: 1.58e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145298      12 KQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLL-EDDKEMLEDLVAAAFNDAARRIEETQKE 90
Cdd:pfam02575   1 KQAQKMQEKMQEAQEELAEKEVEGTSGGGLVKVTVNGKGEVKSIEIDPELVdPEDVEMLEDLIVAAVNDALRKAEELAEE 80

                          90
                  ....*....|
gi 145298      91 KMASVSSGMQ 100
Cdd:pfam02575  81 EMGKLTGGLN 90
PRK14625 PRK14625
hypothetical protein; Provisional
 7-99 1.62e-16

hypothetical protein; Provisional


Pssm-ID: 184772  Cd Length: 109  Bit Score: 68.80  E-value: 1.62e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145298      7 LGNLMKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE-DDKEMLEDLVAAAFNDAARRIE 85
Cdd:PRK14625   4 LGGLMKQAQAMQQKLADAQARLAETTVEGTSGGGMVTVTLMGNGELVRVLMDESLVQpGEGEVIADLIVAAHADAKKKLD 83

                         90
                 ....*....|....
gi 145298     86 ETQKEKMASVSSGM 99
Cdd:PRK14625  84 AKQAQLMQEAAGPM 97
 
Name Accession Description Interval E-value
YbaB COG0718
DNA-binding nucleoid-associated protein YbaB/EfbC [Transcription];
6-102 3.50e-43

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


Pssm-ID: 440482  Cd Length: 100  Bit Score: 136.03  E-value: 3.50e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145298     6 GLGNLMKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE-DDKEMLEDLVAAAFNDAARRI 84
Cdd:COG0718   1 NMGGLMKQAQKMQEKMQEAQEELAELEVEGESGGGLVKVTVNGKGEVKSIEIDPSLLDpEDKEMLEDLIVAAVNDALRKA 80

                        90
                ....*....|....*...
gi 145298    85 EETQKEKMASVSSGMQLP 102
Cdd:COG0718  81 EELAQEEMGKLTGGLNLP 98
DNA_YbaB_EbfC TIGR00103
DNA-binding protein, YbaB/EbfC family; The function of this protein is unknown, but it has ...
 1-105 1.33e-40

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: 129.86  E-value: 1.33e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145298       1 MFGKGgLGNLMKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLEDDKEMLEDLVAAAFNDA 80
Cdd:TIGR00103   1 SFGKN-LGELMKQAQQMQEKMKKLQEEIAQFEVTGKSGAGLVKVTINGNLELKSIEIDPSLLEEDKEALEDMITEALNDA 79

                          90       100
                  ....*....|....*....|....*
gi 145298      81 ARRIEETQKEKMasvSSGMQLPPGF 105
Cdd:TIGR00103  80 VKKVEETYKELM---TSGMPLPPGL 101
YbaB_DNA_bd pfam02575
YbaB/EbfC DNA-binding family; This is a family of DNA-binding proteins. Members of this family ...
 12-100 1.58e-37

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: 121.42  E-value: 1.58e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145298      12 KQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLL-EDDKEMLEDLVAAAFNDAARRIEETQKE 90
Cdd:pfam02575   1 KQAQKMQEKMQEAQEELAEKEVEGTSGGGLVKVTVNGKGEVKSIEIDPELVdPEDVEMLEDLIVAAVNDALRKAEELAEE 80

                          90
                  ....*....|
gi 145298      91 KMASVSSGMQ 100
Cdd:pfam02575  81 EMGKLTGGLN 90
PRK14625 PRK14625
hypothetical protein; Provisional
 7-99 1.62e-16

hypothetical protein; Provisional


Pssm-ID: 184772  Cd Length: 109  Bit Score: 68.80  E-value: 1.62e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145298      7 LGNLMKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE-DDKEMLEDLVAAAFNDAARRIE 85
Cdd:PRK14625   4 LGGLMKQAQAMQQKLADAQARLAETTVEGTSGGGMVTVTLMGNGELVRVLMDESLVQpGEGEVIADLIVAAHADAKKKLD 83

                         90
                 ....*....|....
gi 145298     86 ETQKEKMASVSSGM 99
Cdd:PRK14625  84 AKQAQLMQEAAGPM 97
 
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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