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Conserved domains on  [gi|61742586|gb|AAX55114|]
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hypothetical protein At2g16810 [Arabidopsis thaliana]

Protein Classification

F-box protein( domain architecture ID 17779125)

F-box protein is the substrate-recognition component of an SCF (Skp1-cullin-F-box protein) E3 ubiquitin ligase complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins

CATH:  1.20.1280.50
Gene Ontology:  GO:0019005|GO:0005515|GO:0006511|GO:0016567
PubMed:  31898225|11178263|10581972
SCOP:  4001927

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
F_box_assoc_1 super family cl44343
F-box protein interaction domain; This model describes a large family of plant domains, with ...
 138-273 5.43e-23

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.


The actual alignment was detected with superfamily member TIGR01640:

Pssm-ID: 273726 [Multi-domain]  Cd Length: 230  Bit Score: 94.35  E-value: 5.43e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61742586   138 LRGFIFFTRNLKARIYNPTTRQLVILPTIKESDIIagpPYNILYFICHDPVNDRYKLLCTvsyaSDNDLQNLKSELWIFV 217
Cdd:TIGR01640   4 CDGLICFSYGKRLVVWNPSTGQSRWLPTPKSRRSN---KESDTYFLGYDPIEKQYKVLCF----SDRSGNRNQSEHQVYT 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 61742586   218 LEaGGSWKRVANEFPHHVPSHLDLNMNGVLYFLAWT--DPHTCMLVSFDVRSEEFNTM 273
Cdd:TIGR01640  77 LG-SNSWRTIECSPPHHPLKSRGVCINGVLYYLAYTlkTNPDYFIVSFDVSSERFKEF 133
F-box_AtFBW1-like cd22157
F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) ...
 39-77 7.49e-14

F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) and similar proteins; AtFBW1, also called WD-40-associated F-box protein 1, is an F-box protein that contains four WD-40 repeats, which are separated from each other by a spacer region. Like other F-box proteins, AtFBW1 may be a component of SCF (Skp1 Cdc53 F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. This subfamily also contains many F-box only proteins that do not have any WD repeat. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


:

Pssm-ID: 438928  Cd Length: 39  Bit Score: 64.41  E-value: 7.49e-14
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 61742586  39 RYIPQDLLIEILTRLPPKSVMRFKCVSKFWSSLLSSRYF 77
Cdd:cd22157   1 SSLPDDLVEEILSRLPAKSLLRFRCVCKQWNSLISSPSF 39
 
Name Accession Description Interval E-value
F_box_assoc_1 TIGR01640
F-box protein interaction domain; This model describes a large family of plant domains, with ...
 138-273 5.43e-23

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: 94.35  E-value: 5.43e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61742586   138 LRGFIFFTRNLKARIYNPTTRQLVILPTIKESDIIagpPYNILYFICHDPVNDRYKLLCTvsyaSDNDLQNLKSELWIFV 217
Cdd:TIGR01640   4 CDGLICFSYGKRLVVWNPSTGQSRWLPTPKSRRSN---KESDTYFLGYDPIEKQYKVLCF----SDRSGNRNQSEHQVYT 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 61742586   218 LEaGGSWKRVANEFPHHVPSHLDLNMNGVLYFLAWT--DPHTCMLVSFDVRSEEFNTM 273
Cdd:TIGR01640  77 LG-SNSWRTIECSPPHHPLKSRGVCINGVLYYLAYTlkTNPDYFIVSFDVSSERFKEF 133
F-box_AtFBW1-like cd22157
F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) ...
 39-77 7.49e-14

F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) and similar proteins; AtFBW1, also called WD-40-associated F-box protein 1, is an F-box protein that contains four WD-40 repeats, which are separated from each other by a spacer region. Like other F-box proteins, AtFBW1 may be a component of SCF (Skp1 Cdc53 F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. This subfamily also contains many F-box only proteins that do not have any WD repeat. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438928  Cd Length: 39  Bit Score: 64.41  E-value: 7.49e-14
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 61742586  39 RYIPQDLLIEILTRLPPKSVMRFKCVSKFWSSLLSSRYF 77
Cdd:cd22157   1 SSLPDDLVEEILSRLPAKSLLRFRCVCKQWNSLISSPSF 39
FBA_3 pfam08268
F-box associated domain;
243-276 3.76e-10

F-box associated domain;


Pssm-ID: 285468  Cd Length: 125  Bit Score: 56.53  E-value: 3.76e-10
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 61742586   243 MNGVLYFLAWTDP-HTCMLVSFDVRSEEFNTMQVP 276
Cdd:pfam08268   4 INGVLYYGAWTSDnSKSVIVSFDVRSEKFDFIKLP 38
FBOX smart00256
A Receptor for Ubiquitination Targets;
41-81 5.41e-07

A Receptor for Ubiquitination Targets;


Pssm-ID: 197608  Cd Length: 41  Bit Score: 45.51  E-value: 5.41e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 61742586     41 IPQDLLIEILTRLPPKSVMRFKCVSKFWSSLLSSRYFCNRF 81
Cdd:smart00256   1 LPDEILEEILSKLDPKDLLRLRKVSRKWRSLIDSHDFWFKL 41
F-box pfam00646
F-box domain; This domain is approximately 50 amino acids long, and is usually found in the ...
 41-77 3.38e-06

F-box domain; This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; pfam00560 and pfam07723) and the WD repeat (pfam00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 425796  Cd Length: 43  Bit Score: 43.30  E-value: 3.38e-06
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 61742586    41 IPQDLLIEILTRLPPKSVMRFKCVSKFWSSLLSSRYF 77
Cdd:pfam00646   4 LPDDLLLEILSRLDPKDLLRLSLVSKRWRSLVDSLKL 40
 
Name Accession Description Interval E-value
F_box_assoc_1 TIGR01640
F-box protein interaction domain; This model describes a large family of plant domains, with ...
 138-273 5.43e-23

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: 94.35  E-value: 5.43e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61742586   138 LRGFIFFTRNLKARIYNPTTRQLVILPTIKESDIIagpPYNILYFICHDPVNDRYKLLCTvsyaSDNDLQNLKSELWIFV 217
Cdd:TIGR01640   4 CDGLICFSYGKRLVVWNPSTGQSRWLPTPKSRRSN---KESDTYFLGYDPIEKQYKVLCF----SDRSGNRNQSEHQVYT 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 61742586   218 LEaGGSWKRVANEFPHHVPSHLDLNMNGVLYFLAWT--DPHTCMLVSFDVRSEEFNTM 273
Cdd:TIGR01640  77 LG-SNSWRTIECSPPHHPLKSRGVCINGVLYYLAYTlkTNPDYFIVSFDVSSERFKEF 133
F-box_AtFBW1-like cd22157
F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) ...
 39-77 7.49e-14

F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) and similar proteins; AtFBW1, also called WD-40-associated F-box protein 1, is an F-box protein that contains four WD-40 repeats, which are separated from each other by a spacer region. Like other F-box proteins, AtFBW1 may be a component of SCF (Skp1 Cdc53 F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. This subfamily also contains many F-box only proteins that do not have any WD repeat. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438928  Cd Length: 39  Bit Score: 64.41  E-value: 7.49e-14
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 61742586  39 RYIPQDLLIEILTRLPPKSVMRFKCVSKFWSSLLSSRYF 77
Cdd:cd22157   1 SSLPDDLVEEILSRLPAKSLLRFRCVCKQWNSLISSPSF 39
FBA_3 pfam08268
F-box associated domain;
243-276 3.76e-10

F-box associated domain;


Pssm-ID: 285468  Cd Length: 125  Bit Score: 56.53  E-value: 3.76e-10
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 61742586   243 MNGVLYFLAWTDP-HTCMLVSFDVRSEEFNTMQVP 276
Cdd:pfam08268   4 INGVLYYGAWTSDnSKSVIVSFDVRSEKFDFIKLP 38
FBOX smart00256
A Receptor for Ubiquitination Targets;
41-81 5.41e-07

A Receptor for Ubiquitination Targets;


Pssm-ID: 197608  Cd Length: 41  Bit Score: 45.51  E-value: 5.41e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 61742586     41 IPQDLLIEILTRLPPKSVMRFKCVSKFWSSLLSSRYFCNRF 81
Cdd:smart00256   1 LPDEILEEILSKLDPKDLLRLRKVSRKWRSLIDSHDFWFKL 41
F-box pfam00646
F-box domain; This domain is approximately 50 amino acids long, and is usually found in the ...
 41-77 3.38e-06

F-box domain; This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; pfam00560 and pfam07723) and the WD repeat (pfam00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 425796  Cd Length: 43  Bit Score: 43.30  E-value: 3.38e-06
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 61742586    41 IPQDLLIEILTRLPPKSVMRFKCVSKFWSSLLSSRYF 77
Cdd:pfam00646   4 LPDDLLLEILSRLDPKDLLRLSLVSKRWRSLVDSLKL 40
F-box_AtGID2-like cd22151
F-box domain found in Arabidopsis thaliana F-box protein GID2 and similar proteins; AtGID2, ...
 41-71 2.34e-05

F-box domain found in Arabidopsis thaliana F-box protein GID2 and similar proteins; AtGID2, also called protein SLEEPY 1, is an essential component of the SCF-type E3 ligase complex, SCF(GID2), a complex that positively regulates the gibberellin signaling pathway. Upon gibberellin treatment, the SCF(GID2) complex mediates the ubiquitination and subsequent degradation of DELLA proteins (GAI, RGA and RGL2), some repressors of the gibberellin pathway, leading to the activation of the pathway. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438922  Cd Length: 44  Bit Score: 40.77  E-value: 2.34e-05
                        10        20        30
                ....*....|....*....|....*....|.
gi 61742586  41 IPQDLLIEILTRLPPKSVMRFKCVSKFWSSL 71
Cdd:cd22151   3 LPDDLLQEIFKRLDPKSLARAACVCRRWRAA 33
F-box_AtAFR-like cd22152
F-box domain found in Arabidopsis thaliana protein ATTENUATED FAR-RED RESPONSE (AtAFR) and ...
 41-78 6.06e-05

F-box domain found in Arabidopsis thaliana protein ATTENUATED FAR-RED RESPONSE (AtAFR) and similar proteins; AtAFR, also called SKP1-interacting partner 29 (AtSKIP29), or F-box protein AFR, is a component of SCF (SKP1/ASK-cullin-F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. It is part of the phyA-mediated signaling transduction pathway leading to the regulation of gene expression and hypocotyl elongation in response to red and far-red light exposure. This subfamily also includes many other Arabidopsis thaliana SKP1-interacting partner proteins. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438923  Cd Length: 45  Bit Score: 39.86  E-value: 6.06e-05
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 61742586  41 IPQDLLIEILTRLPPKSVMRFKCVSKFWSSLLSSRYFC 78
Cdd:cd22152   5 LPDDIALQCLARVPRSSHPSLSLVSKSWRSLLSSPELF 42
F-box_SF cd09917
F-box domain superfamily; This short domain is commonly found at the N-terminus of various ...
 41-73 1.40e-04

F-box domain superfamily; This short domain is commonly found at the N-terminus of various proteins, and typically co-occurs with one or more other conserved domains or motifs, such as leucine rich repeats, WD40 repeats, kelch, tub, spry, and others. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. One of the best researched roles of F-box proteins is their participation in SCF (Skp1-Cul1-F-box protein), a multi-protein complex that functions as a ubiquitin E3 ligase, where the role of the F-box protein is to recruit target substrates. Gene families containing the F-box are found greatly expanded in narrow taxonomic lineages, such as flowering plants and nematodes. In this hierarchical classification, many of the subfamilies are named according to their domain architectures.


Pssm-ID: 438852  Cd Length: 35  Bit Score: 38.58  E-value: 1.40e-04
                        10        20        30
                ....*....|....*....|....*....|...
gi 61742586  41 IPQDLLIEILTRLPPKSVMRFKCVSKFWSSLLS 73
Cdd:cd09917   3 LPDEILLKILSYLDPRDLLRLSLVCKRWRELAS 35
 
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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