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Conserved domains on  [gi|30689110|ref|NP_194894|]
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AP2/B3-like transcriptional factor family protein [Arabidopsis thaliana]

Protein Classification

B3 domain-containing protein( domain architecture ID 10659976)

B3 DNA-binding domain-containing protein such as Arabidopsis thaliana REM1 that may play a role in flower development

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 171-243 1.91e-16

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: 72.33  E-value: 1.91e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30689110    171 FVAHVTDSNLREDTLFLPRKFDRSDGLIKGSNKIVLMNEEARTWTLILKFRNSSRTFYMRGGWTSFSMSMGLN 243
Cdd:smart01019   2 FKTLTTSDVSKHGRLVLPKQFAESNGPPLKPKEITLLDPDGKSWKVKLKYRGSSGMFLLTGGWKEFVKANGLK 74
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 14-102 3.01e-16

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: 71.94  E-value: 3.01e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30689110     14 FFQPLLPG---FDSYLNIPVKFFSKRIQGRNEGrTVELRtDASEKTWQVKIQGRR------LTVGWKEFASAHDFRVGDI 84
Cdd:smart01019   1 FFKTLTTSdvsKHGRLVLPKQFAESNGPPLKPK-EITLL-DPDGKSWKVKLKYRGssgmflLTGGWKEFVKANGLKAGDS 78

                           90
                   ....*....|....*...
gi 30689110     85 IVFRHEGSLVFHVTALGP 102
Cdd:smart01019  79 LTFELDGNGEFVVSIFRK 96
 
Name Accession Description Interval E-value
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 171-243 1.91e-16

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: 72.33  E-value: 1.91e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30689110    171 FVAHVTDSNLREDTLFLPRKFDRSDGLIKGSNKIVLMNEEARTWTLILKFRNSSRTFYMRGGWTSFSMSMGLN 243
Cdd:smart01019   2 FKTLTTSDVSKHGRLVLPKQFAESNGPPLKPKEITLLDPDGKSWKVKLKYRGSSGMFLLTGGWKEFVKANGLK 74
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 14-102 3.01e-16

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: 71.94  E-value: 3.01e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30689110     14 FFQPLLPG---FDSYLNIPVKFFSKRIQGRNEGrTVELRtDASEKTWQVKIQGRR------LTVGWKEFASAHDFRVGDI 84
Cdd:smart01019   1 FFKTLTTSdvsKHGRLVLPKQFAESNGPPLKPK-EITLL-DPDGKSWKVKLKYRGssgmflLTGGWKEFVKANGLKAGDS 78

                           90
                   ....*....|....*...
gi 30689110     85 IVFRHEGSLVFHVTALGP 102
Cdd:smart01019  79 LTFELDGNGEFVVSIFRK 96
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 13-98 1.24e-15

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: 70.05  E-value: 1.24e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30689110  13 HFFQPLLP---GFDSYLNIPVKFFsKRIQGRNEGRTVELRtDASEKTWQVKIQGR------RLTVGWKEFASAHDFRVGD 83
Cdd:cd10017   2 LFFKVLTPsdvSSLGRLVLPKKFA-KAHLPPKEGVEVTLE-DPDGKKWTVKLKKRknsgrmVLSGGWKEFVRANGLKEGD 79

                        90
                ....*....|....*.
gi 30689110  84 IIVFRHEGS-LVFHVT 98
Cdd:cd10017  80 FLVFELDGRnSKFKVR 95
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 170-242 8.80e-13

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: 62.78  E-value: 8.80e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30689110   170 CFVAHVTDSNLREDTLFLPRKFDRS-DGLIK-GSNKIVLMNEEARTWTLILKFRNSSRTFYMRGGWTSFSMSMGL 242
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFAREnSGLPKrLSKEITLLDEHGKSWTVKLRYRKKSGRYVLTGGWKEFVKANGL 75
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 170-242 5.33e-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: 60.42  E-value: 5.33e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 30689110 170 CFVAHVTDSN-LREDTLFLPRKFDRSDGLIKGSNKIVLMNEEARTWTLILKFRNSSRTFYMRGGWTSFSMSMGL 242
Cdd:cd10017   2 LFFKVLTPSDvSSLGRLVLPKKFAKAHLPPKEGVEVTLEDPDGKKWTVKLKKRKNSGRMVLSGGWKEFVRANGL 75
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 14-91 1.94e-09

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: 53.53  E-value: 1.94e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30689110    14 FFQPLLP---GFDSYLNIPvKFFSKRIQGRNEGRTVELR-TDASEKTWQVKIQGRR------LTVGWKEFASAHDFRVGD 83
Cdd:pfam02362   1 FFKVLVTsdvLSSGRLVIP-KKFARENSGLPKRLSKEITlLDEHGKSWTVKLRYRKksgryvLTGGWKEFVKANGLKAGD 79


                  ....*...
gi 30689110    84 IIVFRHEG 91
Cdd:pfam02362  80 FLTFKLVG 87
 
Name Accession Description Interval E-value
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 171-243 1.91e-16

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: 72.33  E-value: 1.91e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30689110    171 FVAHVTDSNLREDTLFLPRKFDRSDGLIKGSNKIVLMNEEARTWTLILKFRNSSRTFYMRGGWTSFSMSMGLN 243
Cdd:smart01019   2 FKTLTTSDVSKHGRLVLPKQFAESNGPPLKPKEITLLDPDGKSWKVKLKYRGSSGMFLLTGGWKEFVKANGLK 74
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 14-102 3.01e-16

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: 71.94  E-value: 3.01e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30689110     14 FFQPLLPG---FDSYLNIPVKFFSKRIQGRNEGrTVELRtDASEKTWQVKIQGRR------LTVGWKEFASAHDFRVGDI 84
Cdd:smart01019   1 FFKTLTTSdvsKHGRLVLPKQFAESNGPPLKPK-EITLL-DPDGKSWKVKLKYRGssgmflLTGGWKEFVKANGLKAGDS 78

                           90
                   ....*....|....*...
gi 30689110     85 IVFRHEGSLVFHVTALGP 102
Cdd:smart01019  79 LTFELDGNGEFVVSIFRK 96
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 13-98 1.24e-15

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: 70.05  E-value: 1.24e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30689110  13 HFFQPLLP---GFDSYLNIPVKFFsKRIQGRNEGRTVELRtDASEKTWQVKIQGR------RLTVGWKEFASAHDFRVGD 83
Cdd:cd10017   2 LFFKVLTPsdvSSLGRLVLPKKFA-KAHLPPKEGVEVTLE-DPDGKKWTVKLKKRknsgrmVLSGGWKEFVRANGLKEGD 79

                        90
                ....*....|....*.
gi 30689110  84 IIVFRHEGS-LVFHVT 98
Cdd:cd10017  80 FLVFELDGRnSKFKVR 95
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 170-242 8.80e-13

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: 62.78  E-value: 8.80e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30689110   170 CFVAHVTDSNLREDTLFLPRKFDRS-DGLIK-GSNKIVLMNEEARTWTLILKFRNSSRTFYMRGGWTSFSMSMGL 242
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFAREnSGLPKrLSKEITLLDEHGKSWTVKLRYRKKSGRYVLTGGWKEFVKANGL 75
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 170-242 5.33e-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: 60.42  E-value: 5.33e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 30689110 170 CFVAHVTDSN-LREDTLFLPRKFDRSDGLIKGSNKIVLMNEEARTWTLILKFRNSSRTFYMRGGWTSFSMSMGL 242
Cdd:cd10017   2 LFFKVLTPSDvSSLGRLVLPKKFAKAHLPPKEGVEVTLEDPDGKKWTVKLKKRKNSGRMVLSGGWKEFVRANGL 75
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 14-91 1.94e-09

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: 53.53  E-value: 1.94e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30689110    14 FFQPLLP---GFDSYLNIPvKFFSKRIQGRNEGRTVELR-TDASEKTWQVKIQGRR------LTVGWKEFASAHDFRVGD 83
Cdd:pfam02362   1 FFKVLVTsdvLSSGRLVIP-KKFARENSGLPKRLSKEITlLDEHGKSWTVKLRYRKksgryvLTGGWKEFVKANGLKAGD 79


                  ....*...
gi 30689110    84 IIVFRHEG 91
Cdd:pfam02362  80 FLTFKLVG 87
 
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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