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Conserved domains on  [gi|18400436|ref|NP_565561|]
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Putative BCR, YbaB family COG0718 [Arabidopsis thaliana]

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];
74-174 2.29e-17

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


:

Pssm-ID: 440482  Cd Length: 100  Bit Score: 73.24  E-value: 2.29e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18400436  74 NMQNMyetVKKAQMVvQVEAVRVQKELAAAEFDGYCAGELVKVTLSGNQQPIRTDITEAAME-LGSEKLSQLVTEAYKDA 152
Cdd:COG0718   1 NMGGL---MKQAQKM-QEKMQEAQEELAELEVEGESGGGLVKVTVNGKGEVKSIEIDPSLLDpEDKEMLEDLIVAAVNDA 76

                        90       100
                ....*....|....*....|..
gi 18400436 153 HAKSVVAMKERMSDLAQSLGMP 174
Cdd:COG0718  77 LRKAEELAQEEMGKLTGGLNLP 98
 
Name Accession Description Interval E-value
YbaB COG0718
DNA-binding nucleoid-associated protein YbaB/EfbC [Transcription];
74-174 2.29e-17

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


Pssm-ID: 440482  Cd Length: 100  Bit Score: 73.24  E-value: 2.29e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18400436  74 NMQNMyetVKKAQMVvQVEAVRVQKELAAAEFDGYCAGELVKVTLSGNQQPIRTDITEAAME-LGSEKLSQLVTEAYKDA 152
Cdd:COG0718   1 NMGGL---MKQAQKM-QEKMQEAQEELAELEVEGESGGGLVKVTVNGKGEVKSIEIDPSLLDpEDKEMLEDLIVAAVNDA 76

                        90       100
                ....*....|....*....|..
gi 18400436 153 HAKSVVAMKERMSDLAQSLGMP 174
Cdd:COG0718  77 LRKAEELAQEEMGKLTGGLNLP 98
YbaB_DNA_bd pfam02575
YbaB/EbfC DNA-binding family; This is a family of DNA-binding proteins. Members of this family ...
 83-172 3.88e-17

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: 72.12  E-value: 3.88e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18400436    83 KKAQMVvQVEAVRVQKELAAAEFDGYCAGELVKVTLSGNQQPIRTDITEAAMELG-SEKLSQLVTEAYKDAHAKSVVAMK 161
Cdd:pfam02575   1 KQAQKM-QEKMQEAQEELAEKEVEGTSGGGLVKVTVNGKGEVKSIEIDPELVDPEdVEMLEDLIVAAVNDALRKAEELAE 79

                          90
                  ....*....|.
gi 18400436   162 ERMSDLAQSLG 172
Cdd:pfam02575  80 EEMGKLTGGLN 90
DNA_YbaB_EbfC TIGR00103
DNA-binding protein, YbaB/EbfC family; The function of this protein is unknown, but it has ...
 76-177 2.79e-13

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: 62.45  E-value: 2.79e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18400436    76 QNMYETVKKAQMVvQVEAVRVQKELAAAEFDGYCAGELVKVTLSGNQQPIRTDITEAAMELGSEKLSQLVTEAYKDAHAK 155
Cdd:TIGR00103   4 KNLGELMKQAQQM-QEKMKKLQEEIAQFEVTGKSGAGLVKVTINGNLELKSIEIDPSLLEEDKEALEDMITEALNDAVKK 82

                          90       100
                  ....*....|....*....|..
gi 18400436   156 SVVAMKERMSdlaQSLGMPPGL 177
Cdd:TIGR00103  83 VEETYKELMT---SGMPLPPGL 101
 
Name Accession Description Interval E-value
YbaB COG0718
DNA-binding nucleoid-associated protein YbaB/EfbC [Transcription];
74-174 2.29e-17

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


Pssm-ID: 440482  Cd Length: 100  Bit Score: 73.24  E-value: 2.29e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18400436  74 NMQNMyetVKKAQMVvQVEAVRVQKELAAAEFDGYCAGELVKVTLSGNQQPIRTDITEAAME-LGSEKLSQLVTEAYKDA 152
Cdd:COG0718   1 NMGGL---MKQAQKM-QEKMQEAQEELAELEVEGESGGGLVKVTVNGKGEVKSIEIDPSLLDpEDKEMLEDLIVAAVNDA 76

                        90       100
                ....*....|....*....|..
gi 18400436 153 HAKSVVAMKERMSDLAQSLGMP 174
Cdd:COG0718  77 LRKAEELAQEEMGKLTGGLNLP 98
YbaB_DNA_bd pfam02575
YbaB/EbfC DNA-binding family; This is a family of DNA-binding proteins. Members of this family ...
 83-172 3.88e-17

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: 72.12  E-value: 3.88e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18400436    83 KKAQMVvQVEAVRVQKELAAAEFDGYCAGELVKVTLSGNQQPIRTDITEAAMELG-SEKLSQLVTEAYKDAHAKSVVAMK 161
Cdd:pfam02575   1 KQAQKM-QEKMQEAQEELAEKEVEGTSGGGLVKVTVNGKGEVKSIEIDPELVDPEdVEMLEDLIVAAVNDALRKAEELAE 79

                          90
                  ....*....|.
gi 18400436   162 ERMSDLAQSLG 172
Cdd:pfam02575  80 EEMGKLTGGLN 90
DNA_YbaB_EbfC TIGR00103
DNA-binding protein, YbaB/EbfC family; The function of this protein is unknown, but it has ...
 76-177 2.79e-13

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: 62.45  E-value: 2.79e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18400436    76 QNMYETVKKAQMVvQVEAVRVQKELAAAEFDGYCAGELVKVTLSGNQQPIRTDITEAAMELGSEKLSQLVTEAYKDAHAK 155
Cdd:TIGR00103   4 KNLGELMKQAQQM-QEKMKKLQEEIAQFEVTGKSGAGLVKVTINGNLELKSIEIDPSLLEEDKEALEDMITEALNDAVKK 82

                          90       100
                  ....*....|....*....|..
gi 18400436   156 SVVAMKERMSdlaQSLGMPPGL 177
Cdd:TIGR00103  83 VEETYKELMT---SGMPLPPGL 101
 
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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