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Conserved domains on  [gi|42569068|ref|NP_179217|]
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Transcriptional factor B3 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 ...
 19-112 2.16e-20

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: 83.50  E-value: 2.16e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569068     19 FFKVVQSINVSSENKRALPHDFSRSFTDKELSRKMKIRAQWGNSWEVGISKNPRFY-FMEKSGWEKFVRDNALGNSELLT 97
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGPPLKPKEITLLDPDGKSWKVKLKYRGSSGmFLLTGGWKEFVKANGLKAGDSLT 80

                           90
                   ....*....|....*
gi 42569068     98 FTHKGKMHFTVNIFK 112
Cdd:smart01019  81 FELDGNGEFVVSIFR 95
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 203-291 2.47e-09

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: 53.45  E-value: 2.47e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569068    203 FTILFKQGYLVF---LRIPNSVSKDQVPDEKTV-FKIHHPNGKkSWNVVYL----ERFGAFSGGWRRVVKEYPLAVGDTC 274
Cdd:smart01019   1 FFKTLTTSDVSKhgrLVLPKQFAESNGPPLKPKeITLLDPDGK-SWKVKLKyrgsSGMFLLTGGWKEFVKANGLKAGDSL 79

                           90
                   ....*....|....*..
gi 42569068    275 KFTFIKPKELLLVVSKP 291
Cdd:smart01019  80 TFELDGNGEFVVSIFRK 96
 
Name Accession Description Interval E-value
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 19-112 2.16e-20

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: 83.50  E-value: 2.16e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569068     19 FFKVVQSINVSSENKRALPHDFSRSFTDKELSRKMKIRAQWGNSWEVGISKNPRFY-FMEKSGWEKFVRDNALGNSELLT 97
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGPPLKPKEITLLDPDGKSWKVKLKYRGSSGmFLLTGGWKEFVKANGLKAGDSLT 80

                           90
                   ....*....|....*
gi 42569068     98 FTHKGKMHFTVNIFK 112
Cdd:smart01019  81 FELDGNGEFVVSIFR 95
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 18-112 8.77e-17

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: 73.90  E-value: 8.77e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569068  18 SFFKVVQSINVSSENKRALPHDFSRSFTDKELSRKMKIRAQWGNSWEVGISKNP---RFYFmeKSGWEKFVRDNALGNSE 94
Cdd:cd10017   2 LFFKVLTPSDVSSLGRLVLPKKFAKAHLPPKEGVEVTLEDPDGKKWTVKLKKRKnsgRMVL--SGGWKEFVRANGLKEGD 79

                        90
                ....*....|....*....
gi 42569068  95 LLTFTHKGK-MHFTVNIFK 112
Cdd:cd10017  80 FLVFELDGRnSKFKVRIFR 98
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 19-112 2.44e-16

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: 72.79  E-value: 2.44e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569068    19 FFKVVQSINVSSENKRALPHDFSRSFT--DKELSRKMKIRAQWGNSWEVGIS--KNPRFYFMEKsGWEKFVRDNALGNSE 94
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFARENSglPKRLSKEITLLDEHGKSWTVKLRyrKKSGRYVLTG-GWKEFVKANGLKAGD 79

                          90       100
                  ....*....|....*....|
gi 42569068    95 LLTFTHKGKMHFT--VNIFK 112
Cdd:pfam02362  80 FLTFKLVGNSGFTpvVGIFR 99
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 203-291 2.47e-09

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: 53.45  E-value: 2.47e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569068    203 FTILFKQGYLVF---LRIPNSVSKDQVPDEKTV-FKIHHPNGKkSWNVVYL----ERFGAFSGGWRRVVKEYPLAVGDTC 274
Cdd:smart01019   1 FFKTLTTSDVSKhgrLVLPKQFAESNGPPLKPKeITLLDPDGK-SWKVKLKyrgsSGMFLLTGGWKEFVKANGLKAGDSL 79

                           90
                   ....*....|....*..
gi 42569068    275 KFTFIKPKELLLVVSKP 291
Cdd:smart01019  80 TFELDGNGEFVVSIFRK 96
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 214-287 1.09e-05

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: 43.47  E-value: 1.09e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 42569068 214 FLRIPNSVSKDQVPDEKTV-FKIHHPNGKKsWNVVYLERFG----AFSGGWRRVVKEYPLAVGDTCKFTFIKPKELLLV 287
Cdd:cd10017  17 RLVLPKKFAKAHLPPKEGVeVTLEDPDGKK-WTVKLKKRKNsgrmVLSGGWKEFVRANGLKEGDFLVFELDGRNSKFKV 94
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 215-289 5.24e-05

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: 41.59  E-value: 5.24e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569068   215 LRIPNSVSKDQVPDEKT---VFKIHHPNGKkSWNVVYLE----RFGAFSGGWRRVVKEYPLAVGDTCKFTFIKPKELLLV 287
Cdd:pfam02362  16 LVIPKKFARENSGLPKRlskEITLLDEHGK-SWTVKLRYrkksGRYVLTGGWKEFVKANGLKAGDFLTFKLVGNSGFTPV 94


                  ..
gi 42569068   288 VS 289
Cdd:pfam02362  95 VG 96
 
Name Accession Description Interval E-value
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 19-112 2.16e-20

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: 83.50  E-value: 2.16e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569068     19 FFKVVQSINVSSENKRALPHDFSRSFTDKELSRKMKIRAQWGNSWEVGISKNPRFY-FMEKSGWEKFVRDNALGNSELLT 97
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGPPLKPKEITLLDPDGKSWKVKLKYRGSSGmFLLTGGWKEFVKANGLKAGDSLT 80

                           90
                   ....*....|....*
gi 42569068     98 FTHKGKMHFTVNIFK 112
Cdd:smart01019  81 FELDGNGEFVVSIFR 95
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 18-112 8.77e-17

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: 73.90  E-value: 8.77e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569068  18 SFFKVVQSINVSSENKRALPHDFSRSFTDKELSRKMKIRAQWGNSWEVGISKNP---RFYFmeKSGWEKFVRDNALGNSE 94
Cdd:cd10017   2 LFFKVLTPSDVSSLGRLVLPKKFAKAHLPPKEGVEVTLEDPDGKKWTVKLKKRKnsgRMVL--SGGWKEFVRANGLKEGD 79

                        90
                ....*....|....*....
gi 42569068  95 LLTFTHKGK-MHFTVNIFK 112
Cdd:cd10017  80 FLVFELDGRnSKFKVRIFR 98
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 19-112 2.44e-16

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: 72.79  E-value: 2.44e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569068    19 FFKVVQSINVSSENKRALPHDFSRSFT--DKELSRKMKIRAQWGNSWEVGIS--KNPRFYFMEKsGWEKFVRDNALGNSE 94
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFARENSglPKRLSKEITLLDEHGKSWTVKLRyrKKSGRYVLTG-GWKEFVKANGLKAGD 79

                          90       100
                  ....*....|....*....|
gi 42569068    95 LLTFTHKGKMHFT--VNIFK 112
Cdd:pfam02362  80 FLTFKLVGNSGFTpvVGIFR 99
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 203-291 2.47e-09

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: 53.45  E-value: 2.47e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569068    203 FTILFKQGYLVF---LRIPNSVSKDQVPDEKTV-FKIHHPNGKkSWNVVYL----ERFGAFSGGWRRVVKEYPLAVGDTC 274
Cdd:smart01019   1 FFKTLTTSDVSKhgrLVLPKQFAESNGPPLKPKeITLLDPDGK-SWKVKLKyrgsSGMFLLTGGWKEFVKANGLKAGDSL 79

                           90
                   ....*....|....*..
gi 42569068    275 KFTFIKPKELLLVVSKP 291
Cdd:smart01019  80 TFELDGNGEFVVSIFRK 96
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 214-287 1.09e-05

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: 43.47  E-value: 1.09e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 42569068 214 FLRIPNSVSKDQVPDEKTV-FKIHHPNGKKsWNVVYLERFG----AFSGGWRRVVKEYPLAVGDTCKFTFIKPKELLLV 287
Cdd:cd10017  17 RLVLPKKFAKAHLPPKEGVeVTLEDPDGKK-WTVKLKKRKNsgrmVLSGGWKEFVRANGLKEGDFLVFELDGRNSKFKV 94
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 215-289 5.24e-05

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: 41.59  E-value: 5.24e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569068   215 LRIPNSVSKDQVPDEKT---VFKIHHPNGKkSWNVVYLE----RFGAFSGGWRRVVKEYPLAVGDTCKFTFIKPKELLLV 287
Cdd:pfam02362  16 LVIPKKFARENSGLPKRlskEITLLDEHGK-SWTVKLRYrkksGRYVLTGGWKEFVKANGLKAGDFLTFKLVGNSGFTPV 94


                  ..
gi 42569068   288 VS 289
Cdd:pfam02362  95 VG 96
 
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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