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Conserved domains on  [gi|923538671|ref|XP_013723834|]
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B3 domain-containing protein At5g06250 [Brassica napus]

Protein Classification

B3 domain-containing protein( domain architecture ID 11130478)

B3 domain-containing protein similar to Arabidopsis thaliana transcription factors, NGA1-4, auxin response factor 23 and B3 domain-containing protein REM19

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 49-155 2.44e-32

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: 114.39  E-value: 2.44e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923538671   49 FEKSLTPSDVGKLNRLVIPKQHAEKYFPLNtiisnnaEEKGMLLSFEDESGKCWRFRYSYWNSSQSYVLTKGWSRYVKDK 128
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFARENSGLP-------KRLSKEITLLDEHGKSWTVKLRYRKKSGRYVLTGGWKEFVKAN 73

                          90       100
                  ....*....|....*....|....*..
gi 923538671  129 QLDPADVVFFQRQRSDSRRLFIGWRRR 155
Cdd:pfam02362  74 GLKAGDFLTFKLVGNSGFTPVVGIFRK 100
 
Name Accession Description Interval E-value
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 49-155 2.44e-32

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: 114.39  E-value: 2.44e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923538671   49 FEKSLTPSDVGKLNRLVIPKQHAEKYFPLNtiisnnaEEKGMLLSFEDESGKCWRFRYSYWNSSQSYVLTKGWSRYVKDK 128
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFARENSGLP-------KRLSKEITLLDEHGKSWTVKLRYRKKSGRYVLTGGWKEFVKAN 73

                          90       100
                  ....*....|....*....|....*..
gi 923538671  129 QLDPADVVFFQRQRSDSRRLFIGWRRR 155
Cdd:pfam02362  74 GLKAGDFLTFKLVGNSGFTPVVGIFRK 100
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 48-146 1.15e-26

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: 99.71  E-value: 1.15e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923538671  48 LFEKSLTPSDVGKLNRLVIPKQHAEKYFPLNtiisnnaeeKGMLLSFEDESGKCWRFRYSYWNSSQSYVLTKGWSRYVKD 127
Cdd:cd10017    2 LFFKVLTPSDVSSLGRLVLPKKFAKAHLPPK---------EGVEVTLEDPDGKKWTVKLKKRKNSGRMVLSGGWKEFVRA 72

                         90
                 ....*....|....*....
gi 923538671 128 KQLDPADVVFFQRQRSDSR 146
Cdd:cd10017   73 NGLKEGDFLVFELDGRNSK 91
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 49-148 2.06e-26

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: 98.91  E-value: 2.06e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923538671    49 FEKSLTPSDVGKLNRLVIPKQHAEKYFPlntiisnnaEEKGMLLSFEDESGKCWRFRYSYWNSSQSYVLTKGWSRYVKDK 128
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGP---------PLKPKEITLLDPDGKSWKVKLKYRGSSGMFLLTGGWKEFVKAN 71

                           90       100
                   ....*....|....*....|
gi 923538671   129 QLDPADVVFFQRQRSDSRRL 148
Cdd:smart01019  72 GLKAGDSLTFELDGNGEFVV 91
 
Name Accession Description Interval E-value
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 49-155 2.44e-32

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: 114.39  E-value: 2.44e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923538671   49 FEKSLTPSDVGKLNRLVIPKQHAEKYFPLNtiisnnaEEKGMLLSFEDESGKCWRFRYSYWNSSQSYVLTKGWSRYVKDK 128
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFARENSGLP-------KRLSKEITLLDEHGKSWTVKLRYRKKSGRYVLTGGWKEFVKAN 73

                          90       100
                  ....*....|....*....|....*..
gi 923538671  129 QLDPADVVFFQRQRSDSRRLFIGWRRR 155
Cdd:pfam02362  74 GLKAGDFLTFKLVGNSGFTPVVGIFRK 100
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 48-146 1.15e-26

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: 99.71  E-value: 1.15e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923538671  48 LFEKSLTPSDVGKLNRLVIPKQHAEKYFPLNtiisnnaeeKGMLLSFEDESGKCWRFRYSYWNSSQSYVLTKGWSRYVKD 127
Cdd:cd10017    2 LFFKVLTPSDVSSLGRLVLPKKFAKAHLPPK---------EGVEVTLEDPDGKKWTVKLKKRKNSGRMVLSGGWKEFVRA 72

                         90
                 ....*....|....*....
gi 923538671 128 KQLDPADVVFFQRQRSDSR 146
Cdd:cd10017   73 NGLKEGDFLVFELDGRNSK 91
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 49-148 2.06e-26

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: 98.91  E-value: 2.06e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923538671    49 FEKSLTPSDVGKLNRLVIPKQHAEKYFPlntiisnnaEEKGMLLSFEDESGKCWRFRYSYWNSSQSYVLTKGWSRYVKDK 128
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGP---------PLKPKEITLLDPDGKSWKVKLKYRGSSGMFLLTGGWKEFVKAN 71

                           90       100
                   ....*....|....*....|
gi 923538671   129 QLDPADVVFFQRQRSDSRRL 148
Cdd:smart01019  72 GLKAGDSLTFELDGNGEFVV 91
BfiI_C_EcoRII_N_B3 cd10015
DNA binding domains of BfiI, EcoRII and plant B3 proteins; This family contains the N-terminal ...
 47-142 4.37e-08

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: 50.33  E-value: 4.37e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923538671  47 YLFEKSLTPSDVGK----LNRLVIPKQHAEKYFPLntIISNNAEEKGMLLSFEDES-GKCWRFRYSYWNSSQSYV-LTKG 120
Cdd:cd10015    1 VVLIKRLSANDTGAtgghQVGLYIPKGIVEKFPPS--INHTREANPSIFLTMHDISdCRDWEARAIFYNSNRNEKrLTRG 78

                         90       100
                 ....*....|....*....|..
gi 923538671 121 WSRYVKDKQLDPADVVFFQRQR 142
Cdd:cd10015   79 GRGFVKQNPLNTGDLTLIAFDL 100
At2g31720-like pfam03754
B3 domain-containing protein At2g31720-like; This entry represents a group of uncharacterized ...
 49-127 1.07e-03

B3 domain-containing protein At2g31720-like; This entry represents a group of uncharacterized plant proteins, including B3 domain-containing protein At2g31720 (also known as Protein AUXIN RESPONSE FACTOR 70) from Arabidopsis. These are DNA-binding proteins likely to be involved in stress response.


Pssm-ID: 281714  Cd Length: 113  Bit Score: 37.72  E-value: 1.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923538671   49 FEKSLTPSDVGKL-NRLVIPKQHAEKYFPLN----TIIS----NNAEEKGMLLSFEDESGKCWRFRYSYW--NSSQSYVL 117
Cdd:pfam03754  24 IEKTLFKTDVDPTqSRLSMPFNQLIRNDFLTeeelRIIReedkIKDRDIGVGVILVDQESKKWVLKLKKWdmKGTWNYVL 103

                          90
                  ....*....|
gi 923538671  118 TKGWSRYVKD 127
Cdd:pfam03754 104 VCGWNDVVTA 113
EcoRII_N cd10016
N-terminal domain of type IIE restriction endonuclease EcoRII and similar proteins; N-terminal ...
 46-111 1.40e-03

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: 38.12  E-value: 1.40e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 923538671  46 EYLFEKSLTPSDVGKLNR----LVIPKQHAEKYFPLNTIISNNaEEKGMLLSFEDESGKCWRFRYSYWNS 111
Cdd:cd10016    3 IQVYCKRLSANDTGATGGhqagIYIPKSAAELLFPSNHPDEKN-PNPDLTAKISSHDGPTTESRFIYYNN 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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