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Conserved domains on  [gi|1002288001|ref|XP_015648310|]
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F-box/FBD/LRR-repeat protein At1g13570 [Oryza sativa Japonica Group]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
F-box_SF super family cl45894
F-box domain superfamily; This short domain is commonly found at the N-terminus of various ...
 27-61 1.62e-05

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 cd22160:

Pssm-ID: 459239  Cd Length: 36  Bit Score: 41.89  E-value: 1.62e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1002288001  27 LGSLPLDVLDSILSRLHIHDVVRTSALSRSWRRRW 61
Cdd:cd22160     1 ISDLPDELLCHILSFLPTKDAVKTSVLSKRWRHLW 35
FBD super family cl26765
FBD; This region is found in F-box (pfam00646) and other domain containing plant proteins; it ...
 371-423 6.89e-03

FBD; This region is found in F-box (pfam00646) and other domain containing plant proteins; it is repeated in two family members. Its precise function is unknown, but it is thought to be associated with nuclear processes. In fact, several family members are annotated as being similar to transcription factors.


The actual alignment was detected with superfamily member smart00579:

Pssm-ID: 474857  Cd Length: 72  Bit Score: 35.58  E-value: 6.89e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1002288001  371 NEMHFIEFILSKARVLRVLSLTLASDSLSSIEEAIIDITEYPRASPDAQVIFM 423
Cdd:smart00579  20 EEKELVKYFLENAPCLKKLTISVETSDDEEKLEILKELLSLPRASSSCQVQFL 72
 
Name Accession Description Interval E-value
F-box_AtFBL13-like cd22160
F-box domain found in Arabidopsis thaliana F-box/LRR-repeat protein 13 (AtARP13), 25 (AtARP25) ...
 27-61 1.62e-05

F-box domain found in Arabidopsis thaliana F-box/LRR-repeat protein 13 (AtARP13), 25 (AtARP25) and similar proteins; AtARP13 and AtARP25 belong to the largest subfamily of plant F-box proteins, F-box/LRR-repeat protein (FBLs). It contains tandem leucine-rich repeats (LRRs). Like other F-box proteins, they may be components of SCF (Skp1 Cdc53 F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target 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: 438931  Cd Length: 36  Bit Score: 41.89  E-value: 1.62e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1002288001  27 LGSLPLDVLDSILSRLHIHDVVRTSALSRSWRRRW 61
Cdd:cd22160     1 ISDLPDELLCHILSFLPTKDAVKTSVLSKRWRHLW 35
F-box pfam00646
F-box domain; This domain is approximately 50 amino acids long, and is usually found in the ...
 29-65 2.94e-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: 41.37  E-value: 2.94e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1002288001  29 SLPLDVLDSILSRLHIHDVVRTSALSRSWRRRWESLP 65
Cdd:pfam00646   3 DLPDDLLLEILSRLDPKDLLRLSLVSKRWRSLVDSLK 39
FBOX smart00256
A Receptor for Ubiquitination Targets;
30-58 2.60e-03

A Receptor for Ubiquitination Targets;


Pssm-ID: 197608  Cd Length: 41  Bit Score: 35.88  E-value: 2.60e-03
                           10        20
                   ....*....|....*....|....*....
gi 1002288001   30 LPLDVLDSILSRLHIHDVVRTSALSRSWR 58
Cdd:smart00256   1 LPDEILEEILSKLDPKDLLRLRKVSRKWR 29
FBD smart00579
domain in FBox and BRCT domain containing plant proteins;
371-423 6.89e-03

domain in FBox and BRCT domain containing plant proteins;


Pssm-ID: 214730  Cd Length: 72  Bit Score: 35.58  E-value: 6.89e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1002288001  371 NEMHFIEFILSKARVLRVLSLTLASDSLSSIEEAIIDITEYPRASPDAQVIFM 423
Cdd:smart00579  20 EEKELVKYFLENAPCLKKLTISVETSDDEEKLEILKELLSLPRASSSCQVQFL 72
 
Name Accession Description Interval E-value
F-box_AtFBL13-like cd22160
F-box domain found in Arabidopsis thaliana F-box/LRR-repeat protein 13 (AtARP13), 25 (AtARP25) ...
 27-61 1.62e-05

F-box domain found in Arabidopsis thaliana F-box/LRR-repeat protein 13 (AtARP13), 25 (AtARP25) and similar proteins; AtARP13 and AtARP25 belong to the largest subfamily of plant F-box proteins, F-box/LRR-repeat protein (FBLs). It contains tandem leucine-rich repeats (LRRs). Like other F-box proteins, they may be components of SCF (Skp1 Cdc53 F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target 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: 438931  Cd Length: 36  Bit Score: 41.89  E-value: 1.62e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1002288001  27 LGSLPLDVLDSILSRLHIHDVVRTSALSRSWRRRW 61
Cdd:cd22160     1 ISDLPDELLCHILSFLPTKDAVKTSVLSKRWRHLW 35
F-box pfam00646
F-box domain; This domain is approximately 50 amino acids long, and is usually found in the ...
 29-65 2.94e-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: 41.37  E-value: 2.94e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1002288001  29 SLPLDVLDSILSRLHIHDVVRTSALSRSWRRRWESLP 65
Cdd:pfam00646   3 DLPDDLLLEILSRLDPKDLLRLSLVSKRWRSLVDSLK 39
F-box_SF cd09917
F-box domain superfamily; This short domain is commonly found at the N-terminus of various ...
 29-59 8.85e-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: 37.04  E-value: 8.85e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1002288001  29 SLPLDVLDSILSRLHIHDVVRTSALSRSWRR 59
Cdd:cd09917     2 DLPDEILLKILSYLDPRDLLRLSLVCKRWRE 32
F-box_AtFBW1-like cd22157
F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) ...
 29-59 1.62e-03

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: 36.29  E-value: 1.62e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1002288001  29 SLPLDVLDSILSRLHIHDVVRTSALSRSWRR 59
Cdd:cd22157     2 SLPDDLVEEILSRLPAKSLLRFRCVCKQWNS 32
F-box-like pfam12937
F-box-like; This is an F-box-like family.
 27-59 1.92e-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: 1.92e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1002288001  27 LGSLPLDVLDSILSRLHIHDVVRTSALSRSWRR 59
Cdd:pfam12937   1 LSSLPDEILLQIFSYLDPKDLLRLALVCRRWRE 33
FBOX smart00256
A Receptor for Ubiquitination Targets;
30-58 2.60e-03

A Receptor for Ubiquitination Targets;


Pssm-ID: 197608  Cd Length: 41  Bit Score: 35.88  E-value: 2.60e-03
                           10        20
                   ....*....|....*....|....*....
gi 1002288001   30 LPLDVLDSILSRLHIHDVVRTSALSRSWR 58
Cdd:smart00256   1 LPDEILEEILSKLDPKDLLRLRKVSRKWR 29
FBD smart00579
domain in FBox and BRCT domain containing plant proteins;
371-423 6.89e-03

domain in FBox and BRCT domain containing plant proteins;


Pssm-ID: 214730  Cd Length: 72  Bit Score: 35.58  E-value: 6.89e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1002288001  371 NEMHFIEFILSKARVLRVLSLTLASDSLSSIEEAIIDITEYPRASPDAQVIFM 423
Cdd:smart00579  20 EEKELVKYFLENAPCLKKLTISVETSDDEEKLEILKELLSLPRASSSCQVQFL 72
 
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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