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Conserved domains on  [gi|15220968|ref|NP_175215|]
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F-box and associated interaction domains-containing protein [Arabidopsis thaliana]

Protein Classification

F-box protein( domain architecture ID 18134571)

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:0006511|GO:0019005|GO:0005515
PubMed:  31898225|11178263
SCOP:  4001927

Graphical summary

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List of domain hits

 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 ...
 138-348 1.21e-65

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: 207.21  E-value: 1.21e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220968   138 PSYVHGLISFLYGEEQIICNPSIGKSINLPTLGSSETIIGS---FLGYDPIHAQYKVLCLNKSSL--QFCGHQVLTLGAQ 212
Cdd:TIGR01640   1 VVPCDGLICFSYGKRLVVWNPSTGQSRWLPTPKSRRSNKESdtyFLGYDPIEKQYKVLCFSDRSGnrNQSEHQVYTLGSN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220968   213 ncSWRMIQCPTPHYPGT-TSVCIDGVLYYSASRGFTmHEPLNLVRFDLRTESLEIASVFPEDFKSSV-KPSLINYRGKVA 290
Cdd:TIGR01640  81 --SWRTIECSPPHHPLKsRGVCINGVLYYLAYTLKT-NPDYFIVSFDVSSERFKEFIPLPCGNSDSVdYLSLINYKGKLA 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 15220968   291 VFSKYFCGD-FGLWVLEDAKKQQWSKeqRISIRRGVIGRLPQGLQILGTSDMGEVIFAP 348
Cdd:TIGR01640 158 VLKQKKDTNnFDLWVLNDAGKQEWSK--LFTVPIPPLPDLVDDNFLSGFTDKGEIVLCC 214
F-box_SF super family cl45894
F-box domain superfamily; This short domain is commonly found at the N-terminus of various ...
 12-47 1.15e-06

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.


The actual alignment was detected with superfamily member cd22151:

Pssm-ID: 459239  Cd Length: 44  Bit Score: 44.62  E-value: 1.15e-06
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 15220968  12 DPIPVDVLFEIFLNLPAKFLARFVCVSKLWAKIIRN 47
Cdd:cd22151   1 RKLPDDLLQEIFKRLDPKSLARAACVCRRWRAAARS 36
 
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 ...
 138-348 1.21e-65

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: 207.21  E-value: 1.21e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220968   138 PSYVHGLISFLYGEEQIICNPSIGKSINLPTLGSSETIIGS---FLGYDPIHAQYKVLCLNKSSL--QFCGHQVLTLGAQ 212
Cdd:TIGR01640   1 VVPCDGLICFSYGKRLVVWNPSTGQSRWLPTPKSRRSNKESdtyFLGYDPIEKQYKVLCFSDRSGnrNQSEHQVYTLGSN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220968   213 ncSWRMIQCPTPHYPGT-TSVCIDGVLYYSASRGFTmHEPLNLVRFDLRTESLEIASVFPEDFKSSV-KPSLINYRGKVA 290
Cdd:TIGR01640  81 --SWRTIECSPPHHPLKsRGVCINGVLYYLAYTLKT-NPDYFIVSFDVSSERFKEFIPLPCGNSDSVdYLSLINYKGKLA 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 15220968   291 VFSKYFCGD-FGLWVLEDAKKQQWSKeqRISIRRGVIGRLPQGLQILGTSDMGEVIFAP 348
Cdd:TIGR01640 158 VLKQKKDTNnFDLWVLNDAGKQEWSK--LFTVPIPPLPDLVDDNFLSGFTDKGEIVLCC 214
FBA_3 pfam08268
F-box associated domain;
231-351 1.11e-25

F-box associated domain;


Pssm-ID: 285468  Cd Length: 125  Bit Score: 99.67  E-value: 1.11e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220968   231 SVCIDGVLYYSASRGFtMHEPLnLVRFDLRTESLEIASVfPEDFKSSVKPSLINYRGKVAVFSKYFCGDFGLWVLEDAKK 310
Cdd:pfam08268   1 GICINGVLYYGAWTSD-NSKSV-IVSFDVRSEKFDFIKL-PVPLANDLSSTLINYKGKLAVVSHTSDGGIELWVLEDAEK 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 15220968   311 QQWSKEQRISIRRGVIGRLPQGLQILGTSDMGEVIFAPNYF 351
Cdd:pfam08268  78 HEWSKKIFVLPPSHEHLVDNTDLSVVGTTRTGEIILVLPST 118
F-box_AtGID2-like cd22151
F-box domain found in Arabidopsis thaliana F-box protein GID2 and similar proteins; AtGID2, ...
 12-47 1.15e-06

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: 44.62  E-value: 1.15e-06
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 15220968  12 DPIPVDVLFEIFLNLPAKFLARFVCVSKLWAKIIRN 47
Cdd:cd22151   1 RKLPDDLLQEIFKRLDPKSLARAACVCRRWRAAARS 36
FBOX smart00256
A Receptor for Ubiquitination Targets;
14-50 1.44e-06

A Receptor for Ubiquitination Targets;


Pssm-ID: 197608  Cd Length: 41  Bit Score: 44.35  E-value: 1.44e-06
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 15220968     14 IPVDVLFEIFLNLPAKFLARFVCVSKLWAKIIRNQDF 50
Cdd:smart00256   1 LPDEILEEILSKLDPKDLLRLRKVSRKWRSLIDSHDF 37
F-box pfam00646
F-box domain; This domain is approximately 50 amino acids long, and is usually found in the ...
 14-52 1.42e-05

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: 41.76  E-value: 1.42e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 15220968    14 IPVDVLFEIFLNLPAKFLARFVCVSKLWAKIIRNQDFIR 52
Cdd:pfam00646   4 LPDDLLLEILSRLDPKDLLRLSLVSKRWRSLVDSLKLWK 42
 
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 ...
 138-348 1.21e-65

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: 207.21  E-value: 1.21e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220968   138 PSYVHGLISFLYGEEQIICNPSIGKSINLPTLGSSETIIGS---FLGYDPIHAQYKVLCLNKSSL--QFCGHQVLTLGAQ 212
Cdd:TIGR01640   1 VVPCDGLICFSYGKRLVVWNPSTGQSRWLPTPKSRRSNKESdtyFLGYDPIEKQYKVLCFSDRSGnrNQSEHQVYTLGSN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220968   213 ncSWRMIQCPTPHYPGT-TSVCIDGVLYYSASRGFTmHEPLNLVRFDLRTESLEIASVFPEDFKSSV-KPSLINYRGKVA 290
Cdd:TIGR01640  81 --SWRTIECSPPHHPLKsRGVCINGVLYYLAYTLKT-NPDYFIVSFDVSSERFKEFIPLPCGNSDSVdYLSLINYKGKLA 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 15220968   291 VFSKYFCGD-FGLWVLEDAKKQQWSKeqRISIRRGVIGRLPQGLQILGTSDMGEVIFAP 348
Cdd:TIGR01640 158 VLKQKKDTNnFDLWVLNDAGKQEWSK--LFTVPIPPLPDLVDDNFLSGFTDKGEIVLCC 214
FBA_3 pfam08268
F-box associated domain;
231-351 1.11e-25

F-box associated domain;


Pssm-ID: 285468  Cd Length: 125  Bit Score: 99.67  E-value: 1.11e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15220968   231 SVCIDGVLYYSASRGFtMHEPLnLVRFDLRTESLEIASVfPEDFKSSVKPSLINYRGKVAVFSKYFCGDFGLWVLEDAKK 310
Cdd:pfam08268   1 GICINGVLYYGAWTSD-NSKSV-IVSFDVRSEKFDFIKL-PVPLANDLSSTLINYKGKLAVVSHTSDGGIELWVLEDAEK 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 15220968   311 QQWSKEQRISIRRGVIGRLPQGLQILGTSDMGEVIFAPNYF 351
Cdd:pfam08268  78 HEWSKKIFVLPPSHEHLVDNTDLSVVGTTRTGEIILVLPST 118
F-box_AtGID2-like cd22151
F-box domain found in Arabidopsis thaliana F-box protein GID2 and similar proteins; AtGID2, ...
 12-47 1.15e-06

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: 44.62  E-value: 1.15e-06
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 15220968  12 DPIPVDVLFEIFLNLPAKFLARFVCVSKLWAKIIRN 47
Cdd:cd22151   1 RKLPDDLLQEIFKRLDPKSLARAACVCRRWRAAARS 36
FBOX smart00256
A Receptor for Ubiquitination Targets;
14-50 1.44e-06

A Receptor for Ubiquitination Targets;


Pssm-ID: 197608  Cd Length: 41  Bit Score: 44.35  E-value: 1.44e-06
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 15220968     14 IPVDVLFEIFLNLPAKFLARFVCVSKLWAKIIRNQDF 50
Cdd:smart00256   1 LPDEILEEILSKLDPKDLLRLRKVSRKWRSLIDSHDF 37
F-box_AtFBW1-like cd22157
F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) ...
 14-50 1.76e-06

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: 43.99  E-value: 1.76e-06
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 15220968  14 IPVDVLFEIFLNLPAKFLARFVCVSKLWAKIIRNQDF 50
Cdd:cd22157   3 LPDDLVEEILSRLPAKSLLRFRCVCKQWNSLISSPSF 39
F-box pfam00646
F-box domain; This domain is approximately 50 amino acids long, and is usually found in the ...
 14-52 1.42e-05

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: 41.76  E-value: 1.42e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 15220968    14 IPVDVLFEIFLNLPAKFLARFVCVSKLWAKIIRNQDFIR 52
Cdd:pfam00646   4 LPDDLLLEILSRLDPKDLLRLSLVSKRWRSLVDSLKLWK 42
F-box_SF cd09917
F-box domain superfamily; This short domain is commonly found at the N-terminus of various ...
 14-46 2.39e-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: 37.81  E-value: 2.39e-04
                        10        20        30
                ....*....|....*....|....*....|...
gi 15220968  14 IPVDVLFEIFLNLPAKFLARFVCVSKLWAKIIR 46
Cdd:cd09917   3 LPDEILLKILSYLDPRDLLRLSLVCKRWRELAS 35
F-box-like pfam12937
F-box-like; This is an F-box-like family.
 14-47 2.45e-03

F-box-like; This is an F-box-like family.


Pssm-ID: 463757 [Multi-domain]  Cd Length: 45  Bit Score: 35.54  E-value: 2.45e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15220968    14 IPVDVLFEIFLNLPAKFLARFVCVSKLWAKIIRN 47
Cdd:pfam12937   4 LPDEILLQIFSYLDPKDLLRLALVCRRWRELASD 37
 
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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