SUPERFAMILY 1.75 HMM library and genome assignments server

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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 complex0.032740.0000000001715Least InformativeInherited
Cellular Component (CC)ubiquitin ligase complex0.000000012830InformativeDirect
Cellular Component (CC)cullin-RING ubiquitin ligase complex0.4530.00002639Highly 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 0.0000001588 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 0.125 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) organic substance catabolic process 0.0000000000007197 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.5176 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.8564 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 0.801 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 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 0.1811 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 0.000009232 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.00003367 Informative Direct
Biological Process (BP) cellular response to endogenous stimulus 0.006376 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.7897 Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle 0.1612 Informative Inherited
Biological Process (BP) cation homeostasis 0.6059 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.2369 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.2426 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.4246 Informative Inherited
Biological Process (BP) negative regulation of catalytic activity 0.91 Informative Inherited
Biological Process (BP) synaptic transmission 0.612 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.2165 Informative Inherited
Biological Process (BP) regulation of cell cycle process 0.0112 Informative Inherited
Biological Process (BP) positive regulation of protein metabolic process 0.8223 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 0.4935 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.9863 Informative Inherited
Biological Process (BP) DNA metabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.6513 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.01187 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 1 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.02106 Informative Inherited
Biological Process (BP) response to light stimulus 0.108 Informative Inherited
Biological Process (BP) regulation of cell development 0.1793 Informative Inherited
Biological Process (BP) regulation of growth 0.8477 Informative Inherited
Biological Process (BP) lipid localization 0.007397 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 0.4122 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 0.000000000008217 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.0000000001903 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0.0000000004639 Highly Informative Direct
Biological Process (BP) regulation of proteolysis 0.000000002655 Highly Informative Direct
Biological Process (BP) regulation of protein ubiquitination 0.000000005263 Highly Informative Direct
Biological Process (BP) regulation of striated muscle cell differentiation 0.000002657 Highly Informative Direct
Biological Process (BP) proteasomal protein catabolic process 0.000005691 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 0.000007817 Highly Informative Direct
Biological Process (BP) regulation of ligase activity 0.00001271 Highly Informative Direct
Biological Process (BP) regulation of striated muscle tissue development 0.00005733 Highly Informative Direct
Biological Process (BP) mitotic cell cycle phase transition 0.0002011 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 0.0004815 Highly Informative Direct
Biological Process (BP) cellular response to biotic stimulus 0.1055 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.3664 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle phase transition 0.01146 Highly Informative Inherited
Biological Process (BP) negative regulation of cell cycle 0.1247 Highly Informative Inherited
Biological Process (BP) regulation of mitosis 0.4314 Highly Informative Inherited
Biological Process (BP) negative regulation of cellular catabolic process 0.04228 Highly Informative Inherited
Biological Process (BP) DNA damage checkpoint 0.02772 Highly Informative Inherited
Biological Process (BP) meiosis 0.4754 Highly Informative Inherited
Biological Process (BP) DNA recombination 0.3725 Highly Informative Inherited
Biological Process (BP) regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 0.006027 Highly Informative Inherited
Biological Process (BP) ossification 0.04496 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 0.01138 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 0 Informative Direct
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 0.0005205 Highly Informative Direct
Cellular Component (CC) protein complex 0.0000000001715 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 0.9833 Informative Inherited
Cellular Component (CC) cullin-RING ubiquitin ligase complex 0.00002639 Highly Informative Direct
Cellular Component (CC) centrosome 0.03712 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 phenotype0.3608Least InformativeInherited
Mammalian Phenotype (MP)digestive/alimentary phenotype0.1283Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system physiology0.3456InformativeInherited
Mammalian Phenotype (MP)abnormal cell cycle0.00464Highly 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 cycle0.00001168Moderately InformativeDirect
Biological processBiological rhythms0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processNeurogenesis0.000000000006469InformativeDirect
Biological processMitosis0.00000000004938InformativeDirect
Biological processWnt signaling pathway0.000009013InformativeDirect
Biological processSporulation0.0003931InformativeDirect
Biological processAuxin signaling pathway0.000001839Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCell junction0.0000000002519Moderately InformativeDirect
Cellular componentSynapse0.00004269InformativeDirect
Coding sequence diversityAlternative splicing0.000001173Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainLeucine-rich repeat0InformativeDirect
DomainWD repeat0InformativeDirect
DomainKelch repeat0Highly InformativeDirect
Post-translational modificationReceptor1Moderately InformativeInherited
Post-translational modificationGuanine-nucleotide releasing factor0.0002598InformativeDirect
Post-translational modificationPhotoreceptor protein0.00000661Highly InformativeDirect
Post-translational modificationUbl conjugation0.00008672Moderately 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 ]