SUPERFAMILY 1.75 HMM library and genome assignments server


F-box domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   F-box domain [ 81385]
Superfamily:   F-box domain [ 81383]
Families:   F-box domain [ 81381] (4)


Superfamily statistics
Genomes (523) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 52,245 42,588 6
Proteins 51,212 42,356 6


Functional annotation
General category General
Detailed category Protein interaction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Cellular Component (CC)protein complex0.032439.611e-11Least InformativeInherited
Cellular Component (CC)ubiquitin ligase complex1.104e-080InformativeDirect
Cellular Component (CC)cullin-RING ubiquitin ligase complex0.43432.65e-05Highly InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) protein metabolic process 8.215e-08 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.1013 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) cellular catabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.5132 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.8068 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.7598 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) reproduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.1527 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 1 Moderately Informative Inherited
Biological Process (BP) proteolysis 0 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0 Informative Direct
Biological Process (BP) protein catabolic process 0 Informative Direct
Biological Process (BP) cell cycle process 1.612e-05 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 2.356e-05 Informative Direct
Biological Process (BP) positive regulation of protein modification process 0.9336 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.004714 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.7559 Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle 0.1232 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.2088 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.2288 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.4076 Informative Inherited
Biological Process (BP) negative regulation of catalytic activity 0.8939 Informative Inherited
Biological Process (BP) synaptic transmission 0.5912 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.2009 Informative Inherited
Biological Process (BP) regulation of cell cycle process 0.01446 Informative Inherited
Biological Process (BP) response to DNA damage stimulus 1 Informative Inherited
Biological Process (BP) regulation of system process 1 Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.4903 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.9747 Informative Inherited
Biological Process (BP) DNA metabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.6444 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.02003 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 1 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.01747 Informative Inherited
Biological Process (BP) response to light stimulus 0.1524 Informative Inherited
Biological Process (BP) regulation of cell development 0.1532 Informative Inherited
Biological Process (BP) regulation of growth 0.825 Informative Inherited
Biological Process (BP) lipid localization 0.007086 Informative Inherited
Biological Process (BP) nitrogen compound transport 1 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 1 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.3591 Informative Inherited
Biological Process (BP) protein ubiquitination 0 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 0 Highly Informative Direct
Biological Process (BP) hormone-mediated signaling pathway 6.181e-12 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 3.564e-10 Highly Informative Direct
Biological Process (BP) regulation of protein stability 1.17e-09 Highly Informative Direct
Biological Process (BP) regulation of proteolysis 2.12e-09 Highly Informative Direct
Biological Process (BP) regulation of protein ubiquitination 2.474e-08 Highly Informative Direct
Biological Process (BP) proteasomal protein catabolic process 5.539e-06 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 6.412e-06 Highly Informative Direct
Biological Process (BP) regulation of striated muscle tissue development 2.97e-05 Highly Informative Direct
Biological Process (BP) regulation of ligase activity 7.827e-05 Highly Informative Direct
Biological Process (BP) mitotic cell cycle phase transition 0.0001927 Highly Informative Direct
Biological Process (BP) cellular response to biotic stimulus 0.09733 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.3462 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle phase transition 0.01206 Highly Informative Inherited
Biological Process (BP) negative regulation of cell cycle 0.1167 Highly Informative Inherited
Biological Process (BP) regulation of mitosis 0.3879 Highly Informative Inherited
Biological Process (BP) negative regulation of cellular catabolic process 0.02339 Highly Informative Inherited
Biological Process (BP) DNA damage checkpoint 0.02521 Highly Informative Inherited
Biological Process (BP) meiosis 0.4462 Highly Informative Inherited
Biological Process (BP) DNA recombination 0.3578 Highly Informative Inherited
Biological Process (BP) regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 0.005649 Highly Informative Inherited
Biological Process (BP) ossification 0.04362 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 0.01061 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) cation binding 1 Moderately Informative Inherited
Molecular Function (MF) anion binding 1 Moderately Informative Inherited
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 0 Informative Direct
Molecular Function (MF) transition metal ion binding 1 Informative Inherited
Molecular Function (MF) alcohol binding 0 Highly Informative Direct
Molecular Function (MF) small conjugating protein ligase activity 0 Highly Informative Direct
Molecular Function (MF) iron ion binding 0.000435 Highly Informative Direct
Cellular Component (CC) protein complex 9.611e-11 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoskeleton 1 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 0 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.9774 Informative Inherited
Cellular Component (CC) cullin-RING ubiquitin ligase complex 2.65e-05 Highly Informative Direct
Cellular Component (CC) centrosome 0.03658 Highly Informative Inherited

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.3416Least InformativeInherited
Mammalian Phenotype (MP)digestive/alimentary phenotype0.1249Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system physiology0.3513InformativeInherited
Mammalian Phenotype (MP)abnormal cell cycle0.005011Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant1Least InformativeInherited
Worm Phenotype (WP)protein aggregation variant0.9539Moderately InformativeInherited
Worm Phenotype (WP)protein aggregation induced paralysis0.0004857InformativeDirect
Worm Phenotype (WP)resistant to protein aggregation induced paralysis0.0001297Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0Least InformativeDirect
Zebrafish Anatomy (ZA)cavitated compound organ0Least InformativeDirect
Zebrafish Anatomy (ZA)cell0Least InformativeDirect
Zebrafish Anatomy (ZA)electrically signaling cell0Moderately InformativeDirect
Zebrafish Anatomy (ZA)electrically responsive cell1Moderately InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle1.462e-05Moderately InformativeDirect
Biological processBiological rhythms0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processNeurogenesis6.175e-12InformativeDirect
Biological processMitosis6.313e-11InformativeDirect
Biological processWnt signaling pathway9.077e-06InformativeDirect
Biological processSporulation0.0003949InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCell junction2.492e-10Moderately InformativeDirect
Cellular componentSynapse4.169e-05InformativeDirect
Coding sequence diversityAlternative splicing1.108e-06Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainLeucine-rich repeat0InformativeDirect
DomainWD repeat0InformativeDirect
DomainKelch repeat0Highly InformativeDirect
Post-translational modificationReceptor1Moderately InformativeInherited
Post-translational modificationGuanine-nucleotide releasing factor0.0002609InformativeDirect
Post-translational modificationPhotoreceptor protein6.654e-06Highly InformativeDirect
Post-translational modificationUbl conjugation7.926e-05Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)protein ubiquitination0Moderately InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 5 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a F-box domain domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 5 hidden Markov models representing the F-box domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]