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Conserved domains on  [gi|22329471|ref|NP_683297|]
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B3 DNA-binding domain protein [Arabidopsis thaliana]

Protein Classification

B3 domain-containing protein( domain architecture ID 10178069)

B3 domain-containing protein similar to Arabidopsis thaliana transcription factors: VAL3, FUS3, and LEC2; B3 domain-containing protein such as Arabidopsis thaliana transcription factors, VAL3, FUS3, and LEC2; B3 domain-containing protein such as Arabidopsis thaliana transcription factors, VAL3, FUS3, and LEC2

Gene Ontology:  GO:0003677
PubMed:  25002525|19503786|21155018|18986826

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 22-129 1.93e-12

Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily includes the well-characterized auxin response factor (ARF) and the LAV (Leafy cotyledon2 [LEC2]-Abscisic acid insensitive3 [ABI3]-VAL) families, as well as the RAV (Related to ABI3 and VP1) and REM (REproductive Meristem) families. LEC2 and ABI3 have been shown to be involved in seed development, while other members of the LAV family seem to have a more general role, being expressed in many organs during plant development. Members of the ARF family bind to the auxin response element and depending on presence of an activation or repression domain, they activate or repress transcription. RAV and REM families are less studied B3 protein famillies.


:

Pssm-ID: 197383  Cd Length: 98  Bit Score: 59.65  E-value: 1.93e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22329471  22 WVLKKKLSDSDLYYSAQLYLPKQEMEHFVLPEMdhdlvrklgaGVEVKVRDVDsvDDFYTVRLKVR--NGQYYLGKGWGL 99
Cdd:cd10017   1 PLFFKVLTPSDVSSLGRLVLPKKFAKAHLPPKE----------GVEVTLEDPD--GKKWTVKLKKRknSGRMVLSGGWKE 68

                        90       100       110
                ....*....|....*....|....*....|
gi 22329471 100 IKNAKVLNTGDHIGLFWDKLTREVKFKHFK 129
Cdd:cd10017  69 FVRANGLKEGDFLVFELDGRNSKFKVRIFR 98
 
Name Accession Description Interval E-value
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 22-129 1.93e-12

Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily includes the well-characterized auxin response factor (ARF) and the LAV (Leafy cotyledon2 [LEC2]-Abscisic acid insensitive3 [ABI3]-VAL) families, as well as the RAV (Related to ABI3 and VP1) and REM (REproductive Meristem) families. LEC2 and ABI3 have been shown to be involved in seed development, while other members of the LAV family seem to have a more general role, being expressed in many organs during plant development. Members of the ARF family bind to the auxin response element and depending on presence of an activation or repression domain, they activate or repress transcription. RAV and REM families are less studied B3 protein famillies.


Pssm-ID: 197383  Cd Length: 98  Bit Score: 59.65  E-value: 1.93e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22329471  22 WVLKKKLSDSDLYYSAQLYLPKQEMEHFVLPEMdhdlvrklgaGVEVKVRDVDsvDDFYTVRLKVR--NGQYYLGKGWGL 99
Cdd:cd10017   1 PLFFKVLTPSDVSSLGRLVLPKKFAKAHLPPKE----------GVEVTLEDPD--GKKWTVKLKKRknSGRMVLSGGWKE 68

                        90       100       110
                ....*....|....*....|....*....|
gi 22329471 100 IKNAKVLNTGDHIGLFWDKLTREVKFKHFK 129
Cdd:cd10017  69 FVRANGLKEGDFLVFELDGRNSKFKVRIFR 98
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 25-130 9.09e-11

B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see ) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations.


Pssm-ID: 214977  Cd Length: 96  Bit Score: 54.99  E-value: 9.09e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22329471     25 KKKLSDSDLYYSAQLYLPKQEMEHFVLPEMDHdlvrklgagvEVKVRDVDSVddFYTVRLKVRN--GQYYLGKGWGLIKN 102
Cdd:smart01019   2 FKTLTTSDVSKHGRLVLPKQFAESNGPPLKPK----------EITLLDPDGK--SWKVKLKYRGssGMFLLTGGWKEFVK 69

                           90       100
                   ....*....|....*....|....*...
gi 22329471    103 AKVLNTGDHIGLFWDKlTREVKFKHFKS 130
Cdd:smart01019  70 ANGLKAGDSLTFELDG-NGEFVVSIFRK 96
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 26-110 5.14e-04

B3 DNA binding domain; This is a family of plant transcription factors with various roles in development, the aligned region corresponds the B3 DNA binding domain as described in this domain is found in VP1/AB13 transcription factors. Some proteins also have a second AP2 DNA binding domain pfam00847 such as RAV1. DNA binding activity was demonstrated by.


Pssm-ID: 396783 [Multi-domain]  Cd Length: 101  Bit Score: 37.35  E-value: 5.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22329471    26 KKLSDSDLYYSAQLYLPKQEME-HFVLPEMDhdlvrklgaGVEVKVRDVDSVddFYTVRLKVRN--GQYYLGKGWGLIKN 102
Cdd:pfam02362   3 KVLVTSDVLSSGRLVIPKKFAReNSGLPKRL---------SKEITLLDEHGK--SWTVKLRYRKksGRYVLTGGWKEFVK 71


                  ....*...
gi 22329471   103 AKVLNTGD 110
Cdd:pfam02362  72 ANGLKAGD 79
 
Name Accession Description Interval E-value
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 22-129 1.93e-12

Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily includes the well-characterized auxin response factor (ARF) and the LAV (Leafy cotyledon2 [LEC2]-Abscisic acid insensitive3 [ABI3]-VAL) families, as well as the RAV (Related to ABI3 and VP1) and REM (REproductive Meristem) families. LEC2 and ABI3 have been shown to be involved in seed development, while other members of the LAV family seem to have a more general role, being expressed in many organs during plant development. Members of the ARF family bind to the auxin response element and depending on presence of an activation or repression domain, they activate or repress transcription. RAV and REM families are less studied B3 protein famillies.


Pssm-ID: 197383  Cd Length: 98  Bit Score: 59.65  E-value: 1.93e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22329471  22 WVLKKKLSDSDLYYSAQLYLPKQEMEHFVLPEMdhdlvrklgaGVEVKVRDVDsvDDFYTVRLKVR--NGQYYLGKGWGL 99
Cdd:cd10017   1 PLFFKVLTPSDVSSLGRLVLPKKFAKAHLPPKE----------GVEVTLEDPD--GKKWTVKLKKRknSGRMVLSGGWKE 68

                        90       100       110
                ....*....|....*....|....*....|
gi 22329471 100 IKNAKVLNTGDHIGLFWDKLTREVKFKHFK 129
Cdd:cd10017  69 FVRANGLKEGDFLVFELDGRNSKFKVRIFR 98
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 25-130 9.09e-11

B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see ) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations.


Pssm-ID: 214977  Cd Length: 96  Bit Score: 54.99  E-value: 9.09e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22329471     25 KKKLSDSDLYYSAQLYLPKQEMEHFVLPEMDHdlvrklgagvEVKVRDVDSVddFYTVRLKVRN--GQYYLGKGWGLIKN 102
Cdd:smart01019   2 FKTLTTSDVSKHGRLVLPKQFAESNGPPLKPK----------EITLLDPDGK--SWKVKLKYRGssGMFLLTGGWKEFVK 69

                           90       100
                   ....*....|....*....|....*...
gi 22329471    103 AKVLNTGDHIGLFWDKlTREVKFKHFKS 130
Cdd:smart01019  70 ANGLKAGDSLTFELDG-NGEFVVSIFRK 96
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 26-110 5.14e-04

B3 DNA binding domain; This is a family of plant transcription factors with various roles in development, the aligned region corresponds the B3 DNA binding domain as described in this domain is found in VP1/AB13 transcription factors. Some proteins also have a second AP2 DNA binding domain pfam00847 such as RAV1. DNA binding activity was demonstrated by.


Pssm-ID: 396783 [Multi-domain]  Cd Length: 101  Bit Score: 37.35  E-value: 5.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22329471    26 KKLSDSDLYYSAQLYLPKQEME-HFVLPEMDhdlvrklgaGVEVKVRDVDSVddFYTVRLKVRN--GQYYLGKGWGLIKN 102
Cdd:pfam02362   3 KVLVTSDVLSSGRLVIPKKFAReNSGLPKRL---------SKEITLLDEHGK--SWTVKLRYRKksGRYVLTGGWKEFVK 71


                  ....*...
gi 22329471   103 AKVLNTGD 110
Cdd:pfam02362  72 ANGLKAGD 79
BfiI_C_EcoRII_N_B3 cd10015
DNA binding domains of BfiI, EcoRII and plant B3 proteins; This family contains the N-terminal ...
 23-117 1.33e-03

DNA binding domains of BfiI, EcoRII and plant B3 proteins; This family contains the N-terminal DNA binding domain of type IIE restriction endonuclease EcoRII-like proteins, the C-terminal DNA binding domain of type IIS restriction endonuclease BfiI-like proteins and plant-specific B3 proteins. Type II restriction endonucleases are components of restriction modification (RM) systems that protect bacteria and archaea against invading foreign DNA. They usually function as homodimers or homotetramers that cleave DNA at defined sites of 4 to 8 bp in length, and they require Mg2+, not ATP or GTP, for catalysis. EcoRII is specific for the 5'-CCWGG sequence (W stands for A or T). EcoRII consists of 2 domains, the C-terminal catalytic/dimerization domain (EcoRII-C), and the N-terminal effector DNA binding domain (EcoRII-N). BfiI is unique in cleaving DNA at fixed positions downstream of an asymmetric sequence in the absence of Mg2+. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. B3 proteins are a family of plant-specific transcription factors, involved in a great variety of processes, including seed development and auxin response.


Pssm-ID: 197381  Cd Length: 109  Bit Score: 36.46  E-value: 1.33e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22329471  23 VLKKKLSDSDLYYSAQ----LYLPKQEMEHFvLPEMDHDlvRKLGAGVEVKVRDVDSVDDfYTVRLKVRNG---QYYLGK 95
Cdd:cd10015   2 VLIKRLSANDTGATGGhqvgLYIPKGIVEKF-PPSINHT--REANPSIFLTMHDISDCRD-WEARAIFYNSnrnEKRLTR 77

                        90       100
                ....*....|....*....|..
gi 22329471  96 GWGLIKNAKVLNTGDHIGLFWD 117
Cdd:cd10015  78 GGRGFVKQNPLNTGDLTLIAFD 99
 
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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