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Conserved domains on  [gi|334183743|ref|NP_001185352|]
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uncharacterized protein AT1G68840 [Arabidopsis thaliana]

Protein Classification

B3 domain-containing AP2/ERF family transcription factor( domain architecture ID 11266712)

B3 domain-containing AP2/ERF family transcription factor similar to Arabidopsis thaliana transcription repressors RAV2 and TEM1

Gene Ontology:  GO:0006952|GO:0003700
PubMed:  32522044

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 ...
 188-289 5.71e-33

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: 118.24  E-value: 5.71e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183743  188 FEKAVTPSDVGKLNRLVIPKQHAEKHFPLPSPspavtKGVLINFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNL 267
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFARENSGLPKR-----LSKEITLLDEHGKSWTVKLRYRKKSGRYVLTGGWKEFVKANGL 75

                          90       100
                  ....*....|....*....|..
gi 334183743  268 RAGDVVTFERSTGLERQLYIDW 289
Cdd:pfam02362  76 KAGDFLTFKLVGNSGFTPVVGI 97
AP2 smart00380
DNA-binding domain in plant proteins such as APETALA2 and EREBPs;
64-125 1.07e-27

DNA-binding domain in plant proteins such as APETALA2 and EREBPs;


:

Pssm-ID: 197689  Cd Length: 64  Bit Score: 103.11  E-value: 1.07e-27
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 334183743    64 KYKGVVPQPNGRWGAQIYE--KHQRVWLGTFNEQEEAARSYDIAACRFRGRDAVVNFKNVLEDG 125
Cdd:smart00380   1 KYRGVRQRPWGKWVAEIRDpsKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYDS 64
 
Name Accession Description Interval E-value
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 188-289 5.71e-33

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: 118.24  E-value: 5.71e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183743  188 FEKAVTPSDVGKLNRLVIPKQHAEKHFPLPSPspavtKGVLINFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNL 267
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFARENSGLPKR-----LSKEITLLDEHGKSWTVKLRYRKKSGRYVLTGGWKEFVKANGL 75

                          90       100
                  ....*....|....*....|..
gi 334183743  268 RAGDVVTFERSTGLERQLYIDW 289
Cdd:pfam02362  76 KAGDFLTFKLVGNSGFTPVVGI 97
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 187-278 9.95e-30

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: 109.72  E-value: 9.95e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183743 187 LFEKAVTPSDVGKLNRLVIPKQHAEKHFPLPspspavtKGVLINFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKN 266
Cdd:cd10017    2 LFFKVLTPSDVSSLGRLVLPKKFAKAHLPPK-------EGVEVTLEDPDGKKWTVKLKKRKNSGRMVLSGGWKEFVRANG 74

                         90
                 ....*....|..
gi 334183743 267 LRAGDVVTFERS 278
Cdd:cd10017   75 LKEGDFLVFELD 86
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 188-277 7.19e-29

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: 107.38  E-value: 7.19e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183743   188 FEKAVTPSDVGKLNRLVIPKQHAEKHFPLPSPSPavtkgvlINFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNL 267
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGPPLKPKE-------ITLLDPDGKSWKVKLKYRGSSGMFLLTGGWKEFVKANGL 73

                           90
                   ....*....|
gi 334183743   268 RAGDVVTFER 277
Cdd:smart01019  74 KAGDSLTFEL 83
AP2 smart00380
DNA-binding domain in plant proteins such as APETALA2 and EREBPs;
64-125 1.07e-27

DNA-binding domain in plant proteins such as APETALA2 and EREBPs;


Pssm-ID: 197689  Cd Length: 64  Bit Score: 103.11  E-value: 1.07e-27
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 334183743    64 KYKGVVPQPNGRWGAQIYE--KHQRVWLGTFNEQEEAARSYDIAACRFRGRDAVVNFKNVLEDG 125
Cdd:smart00380   1 KYRGVRQRPWGKWVAEIRDpsKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYDS 64
AP2 cd00018
DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP ...
 63-121 9.16e-27

DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies.


Pssm-ID: 237985  Cd Length: 61  Bit Score: 100.42  E-value: 9.16e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334183743  63 SKYKGVVPQPNGRWGAQIYE--KHQRVWLGTFNEQEEAARSYDIAACRFRGRDAVVNFKNV 121
Cdd:cd00018    1 SKYRGVRQRPWGKWVAEIRDpsGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61
AP2 pfam00847
AP2 domain; This 60 amino acid residue domain can bind to DNA and is found in transcription ...
 64-111 5.50e-04

AP2 domain; This 60 amino acid residue domain can bind to DNA and is found in transcription factor proteins.


Pssm-ID: 425904  Cd Length: 52  Bit Score: 37.61  E-value: 5.50e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 334183743   64 KYKGVVPQPN-GRWGAQIYE----KHQRVWLGTFNEqEEAARSYDIAACRFRG 111
Cdd:pfam00847   1 KIRGVRYDKKwGRWVAEWSEngkrRKKRFSLGKYGT-EEAKRAAIEARKKLEG 52
 
Name Accession Description Interval E-value
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 188-289 5.71e-33

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: 118.24  E-value: 5.71e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183743  188 FEKAVTPSDVGKLNRLVIPKQHAEKHFPLPSPspavtKGVLINFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNL 267
Cdd:pfam02362   1 FFKVLVTSDVLSSGRLVIPKKFARENSGLPKR-----LSKEITLLDEHGKSWTVKLRYRKKSGRYVLTGGWKEFVKANGL 75

                          90       100
                  ....*....|....*....|..
gi 334183743  268 RAGDVVTFERSTGLERQLYIDW 289
Cdd:pfam02362  76 KAGDFLTFKLVGNSGFTPVVGI 97
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 187-278 9.95e-30

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: 109.72  E-value: 9.95e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183743 187 LFEKAVTPSDVGKLNRLVIPKQHAEKHFPLPspspavtKGVLINFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKN 266
Cdd:cd10017    2 LFFKVLTPSDVSSLGRLVLPKKFAKAHLPPK-------EGVEVTLEDPDGKKWTVKLKKRKNSGRMVLSGGWKEFVRANG 74

                         90
                 ....*....|..
gi 334183743 267 LRAGDVVTFERS 278
Cdd:cd10017   75 LKEGDFLVFELD 86
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 188-277 7.19e-29

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: 107.38  E-value: 7.19e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183743   188 FEKAVTPSDVGKLNRLVIPKQHAEKHFPLPSPSPavtkgvlINFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNL 267
Cdd:smart01019   1 FFKTLTTSDVSKHGRLVLPKQFAESNGPPLKPKE-------ITLLDPDGKSWKVKLKYRGSSGMFLLTGGWKEFVKANGL 73

                           90
                   ....*....|
gi 334183743   268 RAGDVVTFER 277
Cdd:smart01019  74 KAGDSLTFEL 83
AP2 smart00380
DNA-binding domain in plant proteins such as APETALA2 and EREBPs;
64-125 1.07e-27

DNA-binding domain in plant proteins such as APETALA2 and EREBPs;


Pssm-ID: 197689  Cd Length: 64  Bit Score: 103.11  E-value: 1.07e-27
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 334183743    64 KYKGVVPQPNGRWGAQIYE--KHQRVWLGTFNEQEEAARSYDIAACRFRGRDAVVNFKNVLEDG 125
Cdd:smart00380   1 KYRGVRQRPWGKWVAEIRDpsKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYDS 64
AP2 cd00018
DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP ...
 63-121 9.16e-27

DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies.


Pssm-ID: 237985  Cd Length: 61  Bit Score: 100.42  E-value: 9.16e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334183743  63 SKYKGVVPQPNGRWGAQIYE--KHQRVWLGTFNEQEEAARSYDIAACRFRGRDAVVNFKNV 121
Cdd:cd00018    1 SKYRGVRQRPWGKWVAEIRDpsGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61
BfiI_C_EcoRII_N_B3 cd10015
DNA binding domains of BfiI, EcoRII and plant B3 proteins; This family contains the N-terminal ...
 186-277 1.67e-12

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: 63.42  E-value: 1.67e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183743 186 VLFEKAVTPSDVGK----LNRLVIPKQHAEKHFPLPSPSPAVTKGVLINFEDVN-GKVWRFRYSYWNSSQSYV-LTKGWS 259
Cdd:cd10015    1 VVLIKRLSANDTGAtgghQVGLYIPKGIVEKFPPSINHTREANPSIFLTMHDISdCRDWEARAIFYNSNRNEKrLTRGGR 80

                         90
                 ....*....|....*...
gi 334183743 260 RFVKEKNLRAGDVVTFER 277
Cdd:cd10015   81 GFVKQNPLNTGDLTLIAF 98
AP2 pfam00847
AP2 domain; This 60 amino acid residue domain can bind to DNA and is found in transcription ...
 64-111 5.50e-04

AP2 domain; This 60 amino acid residue domain can bind to DNA and is found in transcription factor proteins.


Pssm-ID: 425904  Cd Length: 52  Bit Score: 37.61  E-value: 5.50e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 334183743   64 KYKGVVPQPN-GRWGAQIYE----KHQRVWLGTFNEqEEAARSYDIAACRFRG 111
Cdd:pfam00847   1 KIRGVRYDKKwGRWVAEWSEngkrRKKRFSLGKYGT-EEAKRAAIEARKKLEG 52
EcoRII_N cd10016
N-terminal domain of type IIE restriction endonuclease EcoRII and similar proteins; N-terminal ...
 188-320 8.38e-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: 39.28  E-value: 8.38e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183743 188 FEKAVTPSDVGKLNR----LVIPKQHAEKHFPLPSPSPAVT-KGVLINFEDVNGKVWRFRYSYWNSSQS------YVLTK 256
Cdd:cd10016    6 YCKRLSANDTGATGGhqagIYIPKSAAELLFPSNHPDEKNPnPDLTAKISSHDGPTTESRFIYYNNGLFggtrneYRITR 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 334183743 257 --GWSRFVKEKNlrAGDVVTFERSTGLErQLYIDWKVRSGPRENPVQvvvrlfgvDIFNVTTVKPN 320
Cdd:cd10016   86 fgKGFPFLDPDN--TGALLVLAFQSSDC-DLYSVWVCRSDEEEDEFE--------AEIEVLPGALN 140
 
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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