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Conserved domains on  [gi|1063684926|ref|NP_001321214|]
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Transcriptional factor B3 family protein / auxin-responsive factor AUX/IAA-like protein [Arabidopsis thaliana]

Protein Classification

auxin response factor( domain architecture ID 11279093)

auxin response factor (ARF) can function as a transcriptional activator or repressor to regulate the expression of auxin response genes by specifically binding to auxin response elements (AuxREs) during plant development

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Auxin_resp pfam06507
Auxin response factor; A conserved region of auxin-responsive transcription factors.
 279-356 8.30e-41

Auxin response factor; A conserved region of auxin-responsive transcription factors.


:

Pssm-ID: 428981  Cd Length: 83  Bit Score: 144.22  E-value: 8.30e-41
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063684926 279 NRTPFLIFYNPRACPAEFVIPLAKYRKAIcGSQLSVGMRFGMMFETEDSGKRRYMGTIVGISDLDPLRWPGSKWRNLQ 356
Cdd:pfam06507   7 TGSPFTVVYYPRASPSEFVVPYNKVLKAM-NNPWSVGMRFKMRFETEDSSERRYSGTISGVGDADPVRWPGSPWRSLQ 83
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 147-248 6.64e-27

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: 105.07  E-value: 6.64e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684926  147 FCKTLTASDTSTHGGFSVPRRAAEKLFPPLDYsaqpptQELVVRDLHENTWTFRHIYRGQPKRHLLTTGWSLFVGSKRLR 226
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGPPLKP------KEITLLDPDGKSWKVKLKYRGSSGMFLLTGGWKEFVKANGLK 74

                           90       100
                   ....*....|....*....|..
gi 1063684926  227 AGDSVLFIRDEKSQLMVGVRRA 248
Cdd:smart01019  75 AGDSLTFELDGNGEFVVSIFRK 96
AUX_IAA super family cl03528
AUX/IAA family; Transcription of the AUX/IAA family of genes is rapidly induced by the plant ...
 794-862 2.34e-09

AUX/IAA family; Transcription of the AUX/IAA family of genes is rapidly induced by the plant hormone auxin. Some members of this family are longer and contain an N terminal DNA binding domain. The function of this region is uncertain.


The actual alignment was detected with superfamily member pfam02309:

Pssm-ID: 460529  Cd Length: 188  Bit Score: 57.66  E-value: 2.34e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684926 794 GRSIDVTSFKDYEELKSAIECMFG----------------------LEGLLthpQSSGWKLVYVDYESDVLLVGDDPWEE 851
Cdd:pfam02309  90 LRKVDLKAYDSYQELSSALEKMFScftigqcgshgmpgrdglneskLSDLL---DGSEYVLTYEDKDGDWMLVGDVPWEM 166

                          90
                  ....*....|.
gi 1063684926 852 FVGCVRCIRIL 862
Cdd:pfam02309 167 FVDSCKRLRIM 177
 
Name Accession Description Interval E-value
Auxin_resp pfam06507
Auxin response factor; A conserved region of auxin-responsive transcription factors.
 279-356 8.30e-41

Auxin response factor; A conserved region of auxin-responsive transcription factors.


Pssm-ID: 428981  Cd Length: 83  Bit Score: 144.22  E-value: 8.30e-41
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063684926 279 NRTPFLIFYNPRACPAEFVIPLAKYRKAIcGSQLSVGMRFGMMFETEDSGKRRYMGTIVGISDLDPLRWPGSKWRNLQ 356
Cdd:pfam06507   7 TGSPFTVVYYPRASPSEFVVPYNKVLKAM-NNPWSVGMRFKMRFETEDSSERRYSGTISGVGDADPVRWPGSPWRSLQ 83
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 147-248 6.64e-27

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: 105.07  E-value: 6.64e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684926  147 FCKTLTASDTSTHGGFSVPRRAAEKLFPPLDYsaqpptQELVVRDLHENTWTFRHIYRGQPKRHLLTTGWSLFVGSKRLR 226
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGPPLKP------KEITLLDPDGKSWKVKLKYRGSSGMFLLTGGWKEFVKANGLK 74

                           90       100
                   ....*....|....*....|..
gi 1063684926  227 AGDSVLFIRDEKSQLMVGVRRA 248
Cdd:smart01019  75 AGDSLTFELDGNGEFVVSIFRK 96
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 147-249 1.03e-25

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: 102.07  E-value: 1.03e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684926 147 FCKTLTASDTSTHGGFSVPRRAAEKLFPpldySAQPPTQELVVRDLHENTWTFRHIYRGQPKRHLLTTGWSLFVGSKRLR 226
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFARENSG----LPKRLSKEITLLDEHGKSWTVKLRYRKKSGRYVLTGGWKEFVKANGLK 76

                          90       100
                  ....*....|....*....|....*
gi 1063684926 227 AGDSVLF--IRDEKSQLMVGVRRAN 249
Cdd:pfam02362  77 AGDFLTFklVGNSGFTPVVGIFRKS 101
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 146-247 5.52e-23

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: 93.93  E-value: 5.52e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684926 146 FFCKTLTASDTSTHGGFSVPRRAAEKLFPPldysaqPPTQELVVRDLHENTWTFRHIYRGQPKRHLLTTGWSLFVGSKRL 225
Cdd:cd10017     2 LFFKVLTPSDVSSLGRLVLPKKFAKAHLPP------KEGVEVTLEDPDGKKWTVKLKKRKNSGRMVLSGGWKEFVRANGL 75

                          90       100
                  ....*....|....*....|...
gi 1063684926 226 RAGDSVLFIRDEK-SQLMVGVRR 247
Cdd:cd10017    76 KEGDFLVFELDGRnSKFKVRIFR 98
AUX_IAA pfam02309
AUX/IAA family; Transcription of the AUX/IAA family of genes is rapidly induced by the plant ...
 794-862 2.34e-09

AUX/IAA family; Transcription of the AUX/IAA family of genes is rapidly induced by the plant hormone auxin. Some members of this family are longer and contain an N terminal DNA binding domain. The function of this region is uncertain.


Pssm-ID: 460529  Cd Length: 188  Bit Score: 57.66  E-value: 2.34e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684926 794 GRSIDVTSFKDYEELKSAIECMFG----------------------LEGLLthpQSSGWKLVYVDYESDVLLVGDDPWEE 851
Cdd:pfam02309  90 LRKVDLKAYDSYQELSSALEKMFScftigqcgshgmpgrdglneskLSDLL---DGSEYVLTYEDKDGDWMLVGDVPWEM 166

                          90
                  ....*....|.
gi 1063684926 852 FVGCVRCIRIL 862
Cdd:pfam02309 167 FVDSCKRLRIM 177
 
Name Accession Description Interval E-value
Auxin_resp pfam06507
Auxin response factor; A conserved region of auxin-responsive transcription factors.
 279-356 8.30e-41

Auxin response factor; A conserved region of auxin-responsive transcription factors.


Pssm-ID: 428981  Cd Length: 83  Bit Score: 144.22  E-value: 8.30e-41
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063684926 279 NRTPFLIFYNPRACPAEFVIPLAKYRKAIcGSQLSVGMRFGMMFETEDSGKRRYMGTIVGISDLDPLRWPGSKWRNLQ 356
Cdd:pfam06507   7 TGSPFTVVYYPRASPSEFVVPYNKVLKAM-NNPWSVGMRFKMRFETEDSSERRYSGTISGVGDADPVRWPGSPWRSLQ 83
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 147-248 6.64e-27

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: 105.07  E-value: 6.64e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684926  147 FCKTLTASDTSTHGGFSVPRRAAEKLFPPLDYsaqpptQELVVRDLHENTWTFRHIYRGQPKRHLLTTGWSLFVGSKRLR 226
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGPPLKP------KEITLLDPDGKSWKVKLKYRGSSGMFLLTGGWKEFVKANGLK 74

                           90       100
                   ....*....|....*....|..
gi 1063684926  227 AGDSVLFIRDEKSQLMVGVRRA 248
Cdd:smart01019  75 AGDSLTFELDGNGEFVVSIFRK 96
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 147-249 1.03e-25

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: 102.07  E-value: 1.03e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684926 147 FCKTLTASDTSTHGGFSVPRRAAEKLFPpldySAQPPTQELVVRDLHENTWTFRHIYRGQPKRHLLTTGWSLFVGSKRLR 226
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFARENSG----LPKRLSKEITLLDEHGKSWTVKLRYRKKSGRYVLTGGWKEFVKANGLK 76

                          90       100
                  ....*....|....*....|....*
gi 1063684926 227 AGDSVLF--IRDEKSQLMVGVRRAN 249
Cdd:pfam02362  77 AGDFLTFklVGNSGFTPVVGIFRKS 101
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 146-247 5.52e-23

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: 93.93  E-value: 5.52e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684926 146 FFCKTLTASDTSTHGGFSVPRRAAEKLFPPldysaqPPTQELVVRDLHENTWTFRHIYRGQPKRHLLTTGWSLFVGSKRL 225
Cdd:cd10017     2 LFFKVLTPSDVSSLGRLVLPKKFAKAHLPP------KEGVEVTLEDPDGKKWTVKLKKRKNSGRMVLSGGWKEFVRANGL 75

                          90       100
                  ....*....|....*....|...
gi 1063684926 226 RAGDSVLFIRDEK-SQLMVGVRR 247
Cdd:cd10017    76 KEGDFLVFELDGRnSKFKVRIFR 98
AUX_IAA pfam02309
AUX/IAA family; Transcription of the AUX/IAA family of genes is rapidly induced by the plant ...
 794-862 2.34e-09

AUX/IAA family; Transcription of the AUX/IAA family of genes is rapidly induced by the plant hormone auxin. Some members of this family are longer and contain an N terminal DNA binding domain. The function of this region is uncertain.


Pssm-ID: 460529  Cd Length: 188  Bit Score: 57.66  E-value: 2.34e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684926 794 GRSIDVTSFKDYEELKSAIECMFG----------------------LEGLLthpQSSGWKLVYVDYESDVLLVGDDPWEE 851
Cdd:pfam02309  90 LRKVDLKAYDSYQELSSALEKMFScftigqcgshgmpgrdglneskLSDLL---DGSEYVLTYEDKDGDWMLVGDVPWEM 166

                          90
                  ....*....|.
gi 1063684926 852 FVGCVRCIRIL 862
Cdd:pfam02309 167 FVDSCKRLRIM 177
BfiI_C_EcoRII_N_B3 cd10015
DNA binding domains of BfiI, EcoRII and plant B3 proteins; This family contains the N-terminal ...
 147-236 2.92e-07

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: 49.56  E-value: 2.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684926 147 FCKTLTASDTSTHGG----FSVPRRAAEKLFPPLDYSAQ-PPTQELVVRDLHEN-TWTFRHIYRGQPK-RHLLTTGWSLF 219
Cdd:cd10015     3 LIKRLSANDTGATGGhqvgLYIPKGIVEKFPPSINHTREaNPSIFLTMHDISDCrDWEARAIFYNSNRnEKRLTRGGRGF 82

                          90
                  ....*....|....*..
gi 1063684926 220 VGSKRLRAGDSVLFIRD 236
Cdd:cd10015    83 VKQNPLNTGDLTLIAFD 99
EcoRII_N cd10016
N-terminal domain of type IIE restriction endonuclease EcoRII and similar proteins; N-terminal ...
 146-206 1.22e-04

N-terminal domain of type IIE restriction endonuclease EcoRII and similar proteins; N-terminal domain of type IIE restriction endonuclease EcoRII and similar 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). To be catalytically active, EcoRII has to form a dimer.


Pssm-ID: 197382  Cd Length: 142  Bit Score: 43.13  E-value: 1.22e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063684926 146 FFCKTLTASDTSTHG----GFSVPRRAAEKLFPP--LDYSAQPPTQELVVRDLHENTWTFRHIYRGQ 206
Cdd:cd10016     5 VYCKRLSANDTGATGghqaGIYIPKSAAELLFPSnhPDEKNPNPDLTAKISSHDGPTTESRFIYYNN 71
 
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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