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Conserved domains on  [gi|723668719|ref|XP_010315887|]
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auxin response factor 3 isoform X2 [Solanum lycopersicum]

Protein Classification

auxin response factor( domain architecture ID 11130507)

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.
 285-366 2.01e-43

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


:

Pssm-ID: 428981  Cd Length: 83  Bit Score: 151.16  E-value: 2.01e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 723668719  285 AVNVISSRNAFNICYNPRDSSSDFIVPYHKFSKTLAHPFSAGMRFKMRVETEDAAEQRFTGLVVGVSNVDPVRWPGSKWR 364
Cdd:pfam06507   1 AAHAAATGSPFTVVYYPRASPSEFVVPYNKVLKAMNNPWSVGMRFKMRFETEDSSERRYSGTISGVGDADPVRWPGSPWR 80


                  ..
gi 723668719  365 CL 366
Cdd:pfam06507  81 SL 82
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 159-260 8.98e-28

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: 107.46  E-value: 8.98e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 723668719  159 FCKTLTASDTSTHGGFSVPRRAAEDCFaPLDYRQqrpSQELVAKDLHGIEWKFRHIYRGQPRRHLLTTGWSAFVNKKKLV 238
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFARENS-GLPKRL---SKEITLLDEHGKSWTVKLRYRKKSGRYVLTGGWKEFVKANGLK 76

                          90       100
                  ....*....|....*....|....
gi 723668719  239 SGDAVLFLRTGD--GELRLGVRRA 260
Cdd:pfam02362  77 AGDFLTFKLVGNsgFTPVVGIFRK 100
 
Name Accession Description Interval E-value
Auxin_resp pfam06507
Auxin response factor; A conserved region of auxin-responsive transcription factors.
 285-366 2.01e-43

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


Pssm-ID: 428981  Cd Length: 83  Bit Score: 151.16  E-value: 2.01e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 723668719  285 AVNVISSRNAFNICYNPRDSSSDFIVPYHKFSKTLAHPFSAGMRFKMRVETEDAAEQRFTGLVVGVSNVDPVRWPGSKWR 364
Cdd:pfam06507   1 AAHAAATGSPFTVVYYPRASPSEFVVPYNKVLKAMNNPWSVGMRFKMRFETEDSSERRYSGTISGVGDADPVRWPGSPWR 80


                  ..
gi 723668719  365 CL 366
Cdd:pfam06507  81 SL 82
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 159-260 8.98e-28

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: 107.46  E-value: 8.98e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 723668719  159 FCKTLTASDTSTHGGFSVPRRAAEDCFaPLDYRQqrpSQELVAKDLHGIEWKFRHIYRGQPRRHLLTTGWSAFVNKKKLV 238
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFARENS-GLPKRL---SKEITLLDEHGKSWTVKLRYRKKSGRYVLTGGWKEFVKANGLK 76

                          90       100
                  ....*....|....*....|....
gi 723668719  239 SGDAVLFLRTGD--GELRLGVRRA 260
Cdd:pfam02362  77 AGDFLTFKLVGNsgFTPVVGIFRK 100
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 159-260 1.65e-24

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: 98.14  E-value: 1.65e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 723668719   159 FCKTLTASDTSTHGGFSVPRRAAEDCFAPLDyrqqrpSQELVAKDLHGIEWKFRHIYRGQPRRHLLTTGWSAFVNKKKLV 238
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGPPLK------PKEITLLDPDGKSWKVKLKYRGSSGMFLLTGGWKEFVKANGLK 74

                           90       100
                   ....*....|....*....|..
gi 723668719   239 SGDAVLFLRTGDGELRLGVRRA 260
Cdd:smart01019  75 AGDSLTFELDGNGEFVVSIFRK 96
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 157-259 6.84e-21

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: 87.77  E-value: 6.84e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 723668719 157 HMFCKTLTASDTSTHGGFSVPRRAAEDCFAPldyrqqRPSQELVAKDLHGIEWKFRHIYRGQPRRHLLTTGWSAFVNKKK 236
Cdd:cd10017    1 PLFFKVLTPSDVSSLGRLVLPKKFAKAHLPP------KEGVEVTLEDPDGKKWTVKLKKRKNSGRMVLSGGWKEFVRANG 74

                         90       100
                 ....*....|....*....|....
gi 723668719 237 LVSGDAVLFLRTG-DGELRLGVRR 259
Cdd:cd10017   75 LKEGDFLVFELDGrNSKFKVRIFR 98
 
Name Accession Description Interval E-value
Auxin_resp pfam06507
Auxin response factor; A conserved region of auxin-responsive transcription factors.
 285-366 2.01e-43

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


Pssm-ID: 428981  Cd Length: 83  Bit Score: 151.16  E-value: 2.01e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 723668719  285 AVNVISSRNAFNICYNPRDSSSDFIVPYHKFSKTLAHPFSAGMRFKMRVETEDAAEQRFTGLVVGVSNVDPVRWPGSKWR 364
Cdd:pfam06507   1 AAHAAATGSPFTVVYYPRASPSEFVVPYNKVLKAMNNPWSVGMRFKMRFETEDSSERRYSGTISGVGDADPVRWPGSPWR 80


                  ..
gi 723668719  365 CL 366
Cdd:pfam06507  81 SL 82
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 159-260 8.98e-28

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: 107.46  E-value: 8.98e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 723668719  159 FCKTLTASDTSTHGGFSVPRRAAEDCFaPLDYRQqrpSQELVAKDLHGIEWKFRHIYRGQPRRHLLTTGWSAFVNKKKLV 238
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFARENS-GLPKRL---SKEITLLDEHGKSWTVKLRYRKKSGRYVLTGGWKEFVKANGLK 76

                          90       100
                  ....*....|....*....|....
gi 723668719  239 SGDAVLFLRTGD--GELRLGVRRA 260
Cdd:pfam02362  77 AGDFLTFKLVGNsgFTPVVGIFRK 100
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 159-260 1.65e-24

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: 98.14  E-value: 1.65e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 723668719   159 FCKTLTASDTSTHGGFSVPRRAAEDCFAPLDyrqqrpSQELVAKDLHGIEWKFRHIYRGQPRRHLLTTGWSAFVNKKKLV 238
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGPPLK------PKEITLLDPDGKSWKVKLKYRGSSGMFLLTGGWKEFVKANGLK 74

                           90       100
                   ....*....|....*....|..
gi 723668719   239 SGDAVLFLRTGDGELRLGVRRA 260
Cdd:smart01019  75 AGDSLTFELDGNGEFVVSIFRK 96
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 157-259 6.84e-21

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: 87.77  E-value: 6.84e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 723668719 157 HMFCKTLTASDTSTHGGFSVPRRAAEDCFAPldyrqqRPSQELVAKDLHGIEWKFRHIYRGQPRRHLLTTGWSAFVNKKK 236
Cdd:cd10017    1 PLFFKVLTPSDVSSLGRLVLPKKFAKAHLPP------KEGVEVTLEDPDGKKWTVKLKKRKNSGRMVLSGGWKEFVRANG 74

                         90       100
                 ....*....|....*....|....
gi 723668719 237 LVSGDAVLFLRTG-DGELRLGVRR 259
Cdd:cd10017   75 LKEGDFLVFELDGrNSKFKVRIFR 98
BfiI_C_EcoRII_N_B3 cd10015
DNA binding domains of BfiI, EcoRII and plant B3 proteins; This family contains the N-terminal ...
 159-252 2.96e-05

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: 43.78  E-value: 2.96e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 723668719 159 FCKTLTASDTSTHGG----FSVPRRAAEDCFAPLDY-RQQRPSQELVAKDL-HGIEWKFRHIYRGQPR-RHLLTTGWSAF 231
Cdd:cd10015    3 LIKRLSANDTGATGGhqvgLYIPKGIVEKFPPSINHtREANPSIFLTMHDIsDCRDWEARAIFYNSNRnEKRLTRGGRGF 82

                         90       100
                 ....*....|....*....|.
gi 723668719 232 VNKKKLVSGDAVLFLRTGDGE 252
Cdd:cd10015   83 VKQNPLNTGDLTLIAFDLDKE 103
EcoRII_N cd10016
N-terminal domain of type IIE restriction endonuclease EcoRII and similar proteins; N-terminal ...
 159-218 8.19e-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: 40.44  E-value: 8.19e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 723668719 159 FCKTLTASDTSTHG----GFSVPRRAAEDCFAPLDYRQQRPSQELVAK--DLHGIEWKFRHIYRGQ 218
Cdd:cd10016    6 YCKRLSANDTGATGghqaGIYIPKSAAELLFPSNHPDEKNPNPDLTAKisSHDGPTTESRFIYYNN 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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