NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|330252144|gb|AEC07238|]
View 

F-box associated ubiquitination effector family protein [Arabidopsis thaliana]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
FBA_3 super family cl23987
F-box associated domain;
1-70 1.96e-18

F-box associated domain;


The actual alignment was detected with superfamily member pfam08268:

Pssm-ID: 451644  Cd Length: 125  Bit Score: 78.87  E-value: 1.96e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330252144    1 MSFDVRSEKIDLIKGPELPDYNMfmSQKFTSYEGKLAILLTGNGDcSFYMWILEDAAKHEWSKKAYVVPD 70
Cdd:pfam08268  23 VSFDVRSEKFDFIKLPVPLANDL--SSTLINYKGKLAVVSHTSDG-GIELWVLEDAEKHEWSKKIFVLPP 89
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 167-272 1.14e-12

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: 62.73  E-value: 1.14e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330252144 167 IISKTLSRTDVDHHGRLFLPKNQVLSVLKKmrnvtkeslRKGIELEVVDIiENDSYSVILKSRNTTNDFVLASGWSIMKH 246
Cdd:cd10017    2 LFFKVLTPSDVSSLGRLVLPKKFAKAHLPP---------KEGVEVTLEDP-DGKKWTVKLKKRKNSGRMVLSGGWKEFVR 71

                         90       100
                 ....*....|....*....|....*.
gi 330252144 247 SLDLQEGDDIKLFWDYLNYKFIILNF 272
Cdd:cd10017   72 ANGLKEGDFLVFELDGRNSKFKVRIF 97
 
Name Accession Description Interval E-value
FBA_3 pfam08268
F-box associated domain;
1-70 1.96e-18

F-box associated domain;


Pssm-ID: 285468  Cd Length: 125  Bit Score: 78.87  E-value: 1.96e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330252144    1 MSFDVRSEKIDLIKGPELPDYNMfmSQKFTSYEGKLAILLTGNGDcSFYMWILEDAAKHEWSKKAYVVPD 70
Cdd:pfam08268  23 VSFDVRSEKFDFIKLPVPLANDL--SSTLINYKGKLAVVSHTSDG-GIELWVLEDAEKHEWSKKIFVLPP 89
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 167-272 1.14e-12

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: 62.73  E-value: 1.14e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330252144 167 IISKTLSRTDVDHHGRLFLPKNQVLSVLKKmrnvtkeslRKGIELEVVDIiENDSYSVILKSRNTTNDFVLASGWSIMKH 246
Cdd:cd10017    2 LFFKVLTPSDVSSLGRLVLPKKFAKAHLPP---------KEGVEVTLEDP-DGKKWTVKLKKRKNSGRMVLSGGWKEFVR 71

                         90       100
                 ....*....|....*....|....*.
gi 330252144 247 SLDLQEGDDIKLFWDYLNYKFIILNF 272
Cdd:cd10017   72 ANGLKEGDFLVFELDGRNSKFKVRIF 97
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 170-270 2.96e-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: 53.07  E-value: 2.96e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330252144   170 KTLSRTDVDHHGRLFLPKNQVLSVLKKmrnvtkeslRKGIELEVVDIIENdSYSVILKSRNTTNDFVLASGWSIMKHSLD 249
Cdd:smart01019   3 KTLTTSDVSKHGRLVLPKQFAESNGPP---------LKPKEITLLDPDGK-SWKVKLKYRGSSGMFLLTGGWKEFVKANG 72

                           90       100
                   ....*....|....*....|.
gi 330252144   250 LQEGDDIKLFWDYLNYKFIIL 270
Cdd:smart01019  73 LKAGDSLTFELDGNGEFVVSI 93
F_box_assoc_1 TIGR01640
F-box protein interaction domain; This model describes a large family of plant domains, with ...
 1-63 3.67e-08

F-box protein interaction domain; This model describes a large family of plant domains, with several hundred members in Arabidopsis thaliana. Most examples are found C-terminal to an F-box (pfam00646), a 60 amino acid motif involved in ubiquitination of target proteins to mark them for degradation. Two-hybid experiments support the idea that most members are interchangeable F-box subunits of SCF E3 complexes. Some members have two copies of this domain.


Pssm-ID: 273726 [Multi-domain]  Cd Length: 230  Bit Score: 52.75  E-value: 3.67e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 330252144    1 MSFDVRSEKIDL-IKGPEL-PDYNMFMSqkFTSYEGKLAILLTGNGDCSFYMWILEDAAKHEWSK 63
Cdd:TIGR01640 121 VSFDVSSERFKEfIPLPCGnSDSVDYLS--LINYKGKLAVLKQKKDTNNFDLWVLNDAGKQEWSK 183
At2g31720-like pfam03754
B3 domain-containing protein At2g31720-like; This entry represents a group of uncharacterized ...
 156-242 6.32e-04

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: 38.49  E-value: 6.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330252144  156 MMKDFQLDGD--MIISKTLSRTDVDHH-GRLFLPKNQVLSV-------LKKMRNVTKESLRK-GIELEVVDiIENDSYSV 224
Cdd:pfam03754  10 VMRKMNGAEDpkLIIEKTLFKTDVDPTqSRLSMPFNQLIRNdflteeeLRIIREEDKIKDRDiGVGVILVD-QESKKWVL 88

                          90       100
                  ....*....|....*....|
gi 330252144  225 ILKSR--NTTNDFVLASGWS 242
Cdd:pfam03754  89 KLKKWdmKGTWNYVLVCGWN 108
 
Name Accession Description Interval E-value
FBA_3 pfam08268
F-box associated domain;
1-70 1.96e-18

F-box associated domain;


Pssm-ID: 285468  Cd Length: 125  Bit Score: 78.87  E-value: 1.96e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330252144    1 MSFDVRSEKIDLIKGPELPDYNMfmSQKFTSYEGKLAILLTGNGDcSFYMWILEDAAKHEWSKKAYVVPD 70
Cdd:pfam08268  23 VSFDVRSEKFDFIKLPVPLANDL--SSTLINYKGKLAVVSHTSDG-GIELWVLEDAEKHEWSKKIFVLPP 89
B3_DNA cd10017
Plant-specific B3-DNA binding domain; The plant-specific B3 DNA binding domain superfamily ...
 167-272 1.14e-12

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: 62.73  E-value: 1.14e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330252144 167 IISKTLSRTDVDHHGRLFLPKNQVLSVLKKmrnvtkeslRKGIELEVVDIiENDSYSVILKSRNTTNDFVLASGWSIMKH 246
Cdd:cd10017    2 LFFKVLTPSDVSSLGRLVLPKKFAKAHLPP---------KEGVEVTLEDP-DGKKWTVKLKKRKNSGRMVLSGGWKEFVR 71

                         90       100
                 ....*....|....*....|....*.
gi 330252144 247 SLDLQEGDDIKLFWDYLNYKFIILNF 272
Cdd:cd10017   72 ANGLKEGDFLVFELDGRNSKFKVRIF 97
B3 smart01019
B3 DNA binding domain; Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana ...
 170-270 2.96e-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: 53.07  E-value: 2.96e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330252144   170 KTLSRTDVDHHGRLFLPKNQVLSVLKKmrnvtkeslRKGIELEVVDIIENdSYSVILKSRNTTNDFVLASGWSIMKHSLD 249
Cdd:smart01019   3 KTLTTSDVSKHGRLVLPKQFAESNGPP---------LKPKEITLLDPDGK-SWKVKLKYRGSSGMFLLTGGWKEFVKANG 72

                           90       100
                   ....*....|....*....|.
gi 330252144   250 LQEGDDIKLFWDYLNYKFIIL 270
Cdd:smart01019  73 LKAGDSLTFELDGNGEFVVSI 93
F_box_assoc_1 TIGR01640
F-box protein interaction domain; This model describes a large family of plant domains, with ...
 1-63 3.67e-08

F-box protein interaction domain; This model describes a large family of plant domains, with several hundred members in Arabidopsis thaliana. Most examples are found C-terminal to an F-box (pfam00646), a 60 amino acid motif involved in ubiquitination of target proteins to mark them for degradation. Two-hybid experiments support the idea that most members are interchangeable F-box subunits of SCF E3 complexes. Some members have two copies of this domain.


Pssm-ID: 273726 [Multi-domain]  Cd Length: 230  Bit Score: 52.75  E-value: 3.67e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 330252144    1 MSFDVRSEKIDL-IKGPEL-PDYNMFMSqkFTSYEGKLAILLTGNGDCSFYMWILEDAAKHEWSK 63
Cdd:TIGR01640 121 VSFDVSSERFKEfIPLPCGnSDSVDYLS--LINYKGKLAVLKQKKDTNNFDLWVLNDAGKQEWSK 183
At2g31720-like pfam03754
B3 domain-containing protein At2g31720-like; This entry represents a group of uncharacterized ...
 156-242 6.32e-04

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: 38.49  E-value: 6.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330252144  156 MMKDFQLDGD--MIISKTLSRTDVDHH-GRLFLPKNQVLSV-------LKKMRNVTKESLRK-GIELEVVDiIENDSYSV 224
Cdd:pfam03754  10 VMRKMNGAEDpkLIIEKTLFKTDVDPTqSRLSMPFNQLIRNdflteeeLRIIREEDKIKDRDiGVGVILVD-QESKKWVL 88

                          90       100
                  ....*....|....*....|
gi 330252144  225 ILKSR--NTTNDFVLASGWS 242
Cdd:pfam03754  89 KLKKWdmKGTWNYVLVCGWN 108
B3 pfam02362
B3 DNA binding domain; This is a family of plant transcription factors with various roles in ...
 170-254 9.41e-04

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: 37.74  E-value: 9.41e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330252144  170 KTLSRTDVDHHGRLFLPKNQVLSVLKKmrnvtkeSLRKGIELEVVDIiENDSYSVILKSRNTTNDFVLASGWSIMKHSLD 249
Cdd:pfam02362   3 KVLVTSDVLSSGRLVIPKKFARENSGL-------PKRLSKEITLLDE-HGKSWTVKLRYRKKSGRYVLTGGWKEFVKANG 74


                  ....*
gi 330252144  250 LQEGD 254
Cdd:pfam02362  75 LKAGD 79
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH