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Conserved domains on  [gi|75273446|sp|Q9LIR1|]
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RecName: Full=Putative F-box protein At3g23960

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 ...
 126-373 2.94e-55

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: 182.17  E-value: 2.94e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75273446   126 PINGLVSLRGErilkgrirpvDVSIIYNPSTGESLTLPKTNMTRKKIYTVTSFLGYDPIEKQYKVLSMNMSYEKHPKCEg 205
Cdd:TIGR01640   3 PCDGLICFSYG----------KRLVVWNPSTGQSRWLPTPKSRRSNKESDTYFLGYDPIEKQYKVLCFSDRSGNRNQSE- 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75273446   206 YQVLTLGTGklSWRMIKCCLNYqHPLKNSEICINGVLYYLAmVNGSSWPTRAVVCFDIRSEMFNFM----EVYRELSYTT 281
Cdd:TIGR01640  72 HQVYTLGSN--SWRTIECSPPH-HPLKSRGVCINGVLYYLA-YTLKTNPDYFIVSFDVSSERFKEFiplpCGNSDSVDYL 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75273446   282 TLINYnNGKLGMLmgqeaHKTISGicRSFELWVLEDTVKHEWSKHVYLLPPLWKDAVANTrlYFAGMIGTSEIVL-FRPD 360
Cdd:TIGR01640 148 SLINY-KGKLAVL-----KQKKDT--NNFDLWVLNDAGKQEWSKLFTVPIPPLPDLVDDN--FLSGFTDKGEIVLcCEDE 217

                         250
                  ....*....|...
gi 75273446   361 EPLCVFYYNIDRN 373
Cdd:TIGR01640 218 NPFYIFYYNVGEN 230
F-box_SF super family cl45894
F-box domain superfamily; This short domain is commonly found at the N-terminus of various ...
 31-67 2.98e-07

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 cd22157:

Pssm-ID: 459239  Cd Length: 39  Bit Score: 46.30  E-value: 2.98e-07
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 75273446  31 IPIDLLIEIFLKLPVKSIATCRSVSKFWTYVLGRQDF 67
Cdd:cd22157   3 LPDDLVEEILSRLPAKSLLRFRCVCKQWNSLISSPSF 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 ...
 126-373 2.94e-55

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: 182.17  E-value: 2.94e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75273446   126 PINGLVSLRGErilkgrirpvDVSIIYNPSTGESLTLPKTNMTRKKIYTVTSFLGYDPIEKQYKVLSMNMSYEKHPKCEg 205
Cdd:TIGR01640   3 PCDGLICFSYG----------KRLVVWNPSTGQSRWLPTPKSRRSNKESDTYFLGYDPIEKQYKVLCFSDRSGNRNQSE- 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75273446   206 YQVLTLGTGklSWRMIKCCLNYqHPLKNSEICINGVLYYLAmVNGSSWPTRAVVCFDIRSEMFNFM----EVYRELSYTT 281
Cdd:TIGR01640  72 HQVYTLGSN--SWRTIECSPPH-HPLKSRGVCINGVLYYLA-YTLKTNPDYFIVSFDVSSERFKEFiplpCGNSDSVDYL 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75273446   282 TLINYnNGKLGMLmgqeaHKTISGicRSFELWVLEDTVKHEWSKHVYLLPPLWKDAVANTrlYFAGMIGTSEIVL-FRPD 360
Cdd:TIGR01640 148 SLINY-KGKLAVL-----KQKKDT--NNFDLWVLNDAGKQEWSKLFTVPIPPLPDLVDDN--FLSGFTDKGEIVLcCEDE 217

                         250
                  ....*....|...
gi 75273446   361 EPLCVFYYNIDRN 373
Cdd:TIGR01640 218 NPFYIFYYNVGEN 230
FBA_3 pfam08268
F-box associated domain;
236-367 2.18e-38

F-box associated domain;


Pssm-ID: 285468  Cd Length: 125  Bit Score: 134.34  E-value: 2.18e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75273446   236 ICINGVLYYLAMVNGSSwpTRAVVCFDIRSEMFNFMEVYRELSYTT--TLINYNnGKLGmlmgqeahKTISGICRSFELW 313
Cdd:pfam08268   2 ICINGVLYYGAWTSDNS--KSVIVSFDVRSEKFDFIKLPVPLANDLssTLINYK-GKLA--------VVSHTSDGGIELW 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 75273446   314 VLEDTVKHEWSKHVYLLPPLWKDAVANTRLYFAGMIGTSEIVLFRPDEPLCVFY 367
Cdd:pfam08268  71 VLEDAEKHEWSKKIFVLPPSHEHLVDNTDLSVVGTTRTGEIILVLPSTLSKPFY 124
F-box_AtFBW1-like cd22157
F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) ...
 31-67 2.98e-07

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: 46.30  E-value: 2.98e-07
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 75273446  31 IPIDLLIEIFLKLPVKSIATCRSVSKFWTYVLGRQDF 67
Cdd:cd22157   3 LPDDLVEEILSRLPAKSLLRFRCVCKQWNSLISSPSF 39
FBOX smart00256
A Receptor for Ubiquitination Targets;
31-67 3.68e-05

A Receptor for Ubiquitination Targets;


Pssm-ID: 197608  Cd Length: 41  Bit Score: 40.50  E-value: 3.68e-05
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 75273446     31 IPIDLLIEIFLKLPVKSIATCRSVSKFWTYVLGRQDF 67
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 ...
 30-58 1.85e-04

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: 38.67  E-value: 1.85e-04
                          10        20
                  ....*....|....*....|....*....
gi 75273446    30 HIPIDLLIEIFLKLPVKSIATCRSVSKFW 58
Cdd:pfam00646   3 DLPDDLLLEILSRLDPKDLLRLSLVSKRW 31
 
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 ...
 126-373 2.94e-55

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: 182.17  E-value: 2.94e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75273446   126 PINGLVSLRGErilkgrirpvDVSIIYNPSTGESLTLPKTNMTRKKIYTVTSFLGYDPIEKQYKVLSMNMSYEKHPKCEg 205
Cdd:TIGR01640   3 PCDGLICFSYG----------KRLVVWNPSTGQSRWLPTPKSRRSNKESDTYFLGYDPIEKQYKVLCFSDRSGNRNQSE- 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75273446   206 YQVLTLGTGklSWRMIKCCLNYqHPLKNSEICINGVLYYLAmVNGSSWPTRAVVCFDIRSEMFNFM----EVYRELSYTT 281
Cdd:TIGR01640  72 HQVYTLGSN--SWRTIECSPPH-HPLKSRGVCINGVLYYLA-YTLKTNPDYFIVSFDVSSERFKEFiplpCGNSDSVDYL 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75273446   282 TLINYnNGKLGMLmgqeaHKTISGicRSFELWVLEDTVKHEWSKHVYLLPPLWKDAVANTrlYFAGMIGTSEIVL-FRPD 360
Cdd:TIGR01640 148 SLINY-KGKLAVL-----KQKKDT--NNFDLWVLNDAGKQEWSKLFTVPIPPLPDLVDDN--FLSGFTDKGEIVLcCEDE 217

                         250
                  ....*....|...
gi 75273446   361 EPLCVFYYNIDRN 373
Cdd:TIGR01640 218 NPFYIFYYNVGEN 230
FBA_3 pfam08268
F-box associated domain;
236-367 2.18e-38

F-box associated domain;


Pssm-ID: 285468  Cd Length: 125  Bit Score: 134.34  E-value: 2.18e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75273446   236 ICINGVLYYLAMVNGSSwpTRAVVCFDIRSEMFNFMEVYRELSYTT--TLINYNnGKLGmlmgqeahKTISGICRSFELW 313
Cdd:pfam08268   2 ICINGVLYYGAWTSDNS--KSVIVSFDVRSEKFDFIKLPVPLANDLssTLINYK-GKLA--------VVSHTSDGGIELW 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 75273446   314 VLEDTVKHEWSKHVYLLPPLWKDAVANTRLYFAGMIGTSEIVLFRPDEPLCVFY 367
Cdd:pfam08268  71 VLEDAEKHEWSKKIFVLPPSHEHLVDNTDLSVVGTTRTGEIILVLPSTLSKPFY 124
F-box_AtFBW1-like cd22157
F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) ...
 31-67 2.98e-07

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: 46.30  E-value: 2.98e-07
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 75273446  31 IPIDLLIEIFLKLPVKSIATCRSVSKFWTYVLGRQDF 67
Cdd:cd22157   3 LPDDLVEEILSRLPAKSLLRFRCVCKQWNSLISSPSF 39
FBOX smart00256
A Receptor for Ubiquitination Targets;
31-67 3.68e-05

A Receptor for Ubiquitination Targets;


Pssm-ID: 197608  Cd Length: 41  Bit Score: 40.50  E-value: 3.68e-05
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 75273446     31 IPIDLLIEIFLKLPVKSIATCRSVSKFWTYVLGRQDF 67
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 ...
 30-58 1.85e-04

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: 38.67  E-value: 1.85e-04
                          10        20
                  ....*....|....*....|....*....
gi 75273446    30 HIPIDLLIEIFLKLPVKSIATCRSVSKFW 58
Cdd:pfam00646   3 DLPDDLLLEILSRLDPKDLLRLSLVSKRW 31
F-box_SF cd09917
F-box domain superfamily; This short domain is commonly found at the N-terminus of various ...
 30-58 4.09e-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: 37.42  E-value: 4.09e-04
                        10        20
                ....*....|....*....|....*....
gi 75273446  30 HIPIDLLIEIFLKLPVKSIATCRSVSKFW 58
Cdd:cd09917   2 DLPDEILLKILSYLDPRDLLRLSLVCKRW 30
F-box-like pfam12937
F-box-like; This is an F-box-like family.
 30-58 1.22e-03

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


Pssm-ID: 463757 [Multi-domain]  Cd Length: 45  Bit Score: 36.31  E-value: 1.22e-03
                          10        20
                  ....*....|....*....|....*....
gi 75273446    30 HIPIDLLIEIFLKLPVKSIATCRSVSKFW 58
Cdd:pfam12937   3 SLPDEILLQIFSYLDPKDLLRLALVCRRW 31
 
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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