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Conserved domains on  [gi|494328697|ref|WP_007182071|]
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MULTISPECIES: YbaB/EbfC family nucleoid-associated protein [Burkholderiaceae]

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

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List of domain hits

 Name Accession Description Interval E-value
YbaB COG0718
DNA-binding nucleoid-associated protein YbaB/EfbC [Transcription];
5-101 4.87e-42

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


:

Pssm-ID: 440482  Cd Length: 100  Bit Score: 133.33  E-value: 4.87e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494328697   5 QLAGLMKQAQQMQENMKKMQEQLALIEVEGQSGAGLVKVTMTCKNDVRRVSIDPSLL-ADDKDMLEDLVAAAFNDAVRKA 83
Cdd:COG0718    1 NMGGLMKQAQKMQEKMQEAQEELAELEVEGESGGGLVKVTVNGKGEVKSIEIDPSLLdPEDKEMLEDLIVAAVNDALRKA 80

                         90
                 ....*....|....*...
gi 494328697  84 EATAQEKMGGMTSGLPLP 101
Cdd:COG0718   81 EELAQEEMGKLTGGLNLP 98
 
Name Accession Description Interval E-value
YbaB COG0718
DNA-binding nucleoid-associated protein YbaB/EfbC [Transcription];
5-101 4.87e-42

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


Pssm-ID: 440482  Cd Length: 100  Bit Score: 133.33  E-value: 4.87e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494328697   5 QLAGLMKQAQQMQENMKKMQEQLALIEVEGQSGAGLVKVTMTCKNDVRRVSIDPSLL-ADDKDMLEDLVAAAFNDAVRKA 83
Cdd:COG0718    1 NMGGLMKQAQKMQEKMQEAQEELAELEVEGESGGGLVKVTVNGKGEVKSIEIDPSLLdPEDKEMLEDLIVAAVNDALRKA 80

                         90
                 ....*....|....*...
gi 494328697  84 EATAQEKMGGMTSGLPLP 101
Cdd:COG0718   81 EELAQEEMGKLTGGLNLP 98
YbaB_DNA_bd pfam02575
YbaB/EbfC DNA-binding family; This is a family of DNA-binding proteins. Members of this family ...
 11-99 4.39e-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: 120.27  E-value: 4.39e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494328697   11 KQAQQMQENMKKMQEQLALIEVEGQSGAGLVKVTMTCKNDVRRVSIDPSLL-ADDKDMLEDLVAAAFNDAVRKAEATAQE 89
Cdd:pfam02575   1 KQAQKMQEKMQEAQEELAEKEVEGTSGGGLVKVTVNGKGEVKSIEIDPELVdPEDVEMLEDLIVAAVNDALRKAEELAEE 80

                          90
                  ....*....|
gi 494328697   90 KMGGMTSGLP 99
Cdd:pfam02575  81 EMGKLTGGLN 90
DNA_YbaB_EbfC TIGR00103
DNA-binding protein, YbaB/EbfC family; The function of this protein is unknown, but it has ...
 1-104 1.87e-31

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: 106.75  E-value: 1.87e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494328697    1 MMKGQLAGLMKQAQQMQENMKKMQEQLALIEVEGQSGAGLVKVTMTCKNDVRRVSIDPSLLADDKDMLEDLVAAAFNDAV 80
Cdd:TIGR00103   1 SFGKNLGELMKQAQQMQEKMKKLQEEIAQFEVTGKSGAGLVKVTINGNLELKSIEIDPSLLEEDKEALEDMITEALNDAV 80

                          90       100
                  ....*....|....*....|....
gi 494328697   81 RKAEATAQEKmggMTSGLPLPPGF 104
Cdd:TIGR00103  81 KKVEETYKEL---MTSGMPLPPGL 101
PRK14625 PRK14625
hypothetical protein; Provisional
 6-99 8.95e-13

hypothetical protein; Provisional


Pssm-ID: 184772  Cd Length: 109  Bit Score: 59.17  E-value: 8.95e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494328697   6 LAGLMKQAQQMQENMKKMQEQLALIEVEGQSGAGLVKVTMTCKNDVRRVSIDPSLLA-DDKDMLEDLVAAAFNDAVRKAE 84
Cdd:PRK14625   4 LGGLMKQAQAMQQKLADAQARLAETTVEGTSGGGMVTVTLMGNGELVRVLMDESLVQpGEGEVIADLIVAAHADAKKKLD 83

                         90       100
                 ....*....|....*....|..
gi 494328697  85 ATAQE-------KMGGMTSGLP 99
Cdd:PRK14625  84 AKQAQlmqeaagPMAGLMGGLP 105
 
Name Accession Description Interval E-value
YbaB COG0718
DNA-binding nucleoid-associated protein YbaB/EfbC [Transcription];
5-101 4.87e-42

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


Pssm-ID: 440482  Cd Length: 100  Bit Score: 133.33  E-value: 4.87e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494328697   5 QLAGLMKQAQQMQENMKKMQEQLALIEVEGQSGAGLVKVTMTCKNDVRRVSIDPSLL-ADDKDMLEDLVAAAFNDAVRKA 83
Cdd:COG0718    1 NMGGLMKQAQKMQEKMQEAQEELAELEVEGESGGGLVKVTVNGKGEVKSIEIDPSLLdPEDKEMLEDLIVAAVNDALRKA 80

                         90
                 ....*....|....*...
gi 494328697  84 EATAQEKMGGMTSGLPLP 101
Cdd:COG0718   81 EELAQEEMGKLTGGLNLP 98
YbaB_DNA_bd pfam02575
YbaB/EbfC DNA-binding family; This is a family of DNA-binding proteins. Members of this family ...
 11-99 4.39e-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: 120.27  E-value: 4.39e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494328697   11 KQAQQMQENMKKMQEQLALIEVEGQSGAGLVKVTMTCKNDVRRVSIDPSLL-ADDKDMLEDLVAAAFNDAVRKAEATAQE 89
Cdd:pfam02575   1 KQAQKMQEKMQEAQEELAEKEVEGTSGGGLVKVTVNGKGEVKSIEIDPELVdPEDVEMLEDLIVAAVNDALRKAEELAEE 80

                          90
                  ....*....|
gi 494328697   90 KMGGMTSGLP 99
Cdd:pfam02575  81 EMGKLTGGLN 90
DNA_YbaB_EbfC TIGR00103
DNA-binding protein, YbaB/EbfC family; The function of this protein is unknown, but it has ...
 1-104 1.87e-31

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: 106.75  E-value: 1.87e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494328697    1 MMKGQLAGLMKQAQQMQENMKKMQEQLALIEVEGQSGAGLVKVTMTCKNDVRRVSIDPSLLADDKDMLEDLVAAAFNDAV 80
Cdd:TIGR00103   1 SFGKNLGELMKQAQQMQEKMKKLQEEIAQFEVTGKSGAGLVKVTINGNLELKSIEIDPSLLEEDKEALEDMITEALNDAV 80

                          90       100
                  ....*....|....*....|....
gi 494328697   81 RKAEATAQEKmggMTSGLPLPPGF 104
Cdd:TIGR00103  81 KKVEETYKEL---MTSGMPLPPGL 101
PRK14625 PRK14625
hypothetical protein; Provisional
 6-99 8.95e-13

hypothetical protein; Provisional


Pssm-ID: 184772  Cd Length: 109  Bit Score: 59.17  E-value: 8.95e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494328697   6 LAGLMKQAQQMQENMKKMQEQLALIEVEGQSGAGLVKVTMTCKNDVRRVSIDPSLLA-DDKDMLEDLVAAAFNDAVRKAE 84
Cdd:PRK14625   4 LGGLMKQAQAMQQKLADAQARLAETTVEGTSGGGMVTVTLMGNGELVRVLMDESLVQpGEGEVIADLIVAAHADAKKKLD 83

                         90       100
                 ....*....|....*....|..
gi 494328697  85 ATAQE-------KMGGMTSGLP 99
Cdd:PRK14625  84 AKQAQlmqeaagPMAGLMGGLP 105
 
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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