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 (512) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 50,417 42,588 6
Proteins 49,408 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 complex0.029930.00000000002107Least InformativeInherited
Cellular Component (CC)ubiquitin ligase complex0.000000010440InformativeDirect
Cellular Component (CC)cullin-RING ubiquitin ligase complex0.43310.00002849Highly 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 0.00000004928 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 0.07415 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 0.0000000000001474 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.562 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.8261 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 0.6748 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 0.09201 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 0.00001094 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.00001626 Informative Direct
Biological Process (BP) positive regulation of protein modification process 0.8592 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.003002 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.8222 Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle 0.1063 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.1737 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.1886 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.3297 Informative Inherited
Biological Process (BP) cell-cell signaling 1 Informative Inherited
Biological Process (BP) negative regulation of catalytic activity 0.8725 Informative Inherited
Biological Process (BP) transmission of nerve impulse 0.8291 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.1471 Informative Inherited
Biological Process (BP) regulation of cell cycle process 0.01422 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 0.4943 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.9485 Informative Inherited
Biological Process (BP) DNA metabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.6065 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.01476 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 1 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.00914 Informative Inherited
Biological Process (BP) response to light stimulus 0.1315 Informative Inherited
Biological Process (BP) regulation of cell development 0.1229 Informative Inherited
Biological Process (BP) regulation of growth 0.7726 Informative Inherited
Biological Process (BP) lipid localization 0.005913 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 0.3535 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 0.000000000005762 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0.0000000001278 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.0000000007794 Highly Informative Direct
Biological Process (BP) regulation of proteolysis 0.000000006859 Highly Informative Direct
Biological Process (BP) regulation of protein ubiquitination 0.00000001781 Highly Informative Direct
Biological Process (BP) proteasomal protein catabolic process 0.000003509 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 0.00001598 Highly Informative Direct
Biological Process (BP) regulation of striated muscle tissue development 0.00002366 Highly Informative Direct
Biological Process (BP) mitotic cell cycle phase transition 0.000221 Highly Informative Direct
Biological Process (BP) regulation of ligase activity 0.0004033 Highly Informative Direct
Biological Process (BP) negative regulation of growth 0.0005818 Highly Informative Direct
Biological Process (BP) cellular response to biotic stimulus 0.08338 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.3201 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle phase transition 0.01118 Highly Informative Inherited
Biological Process (BP) negative regulation of cell cycle 0.1037 Highly Informative Inherited
Biological Process (BP) regulation of mitosis 0.3834 Highly Informative Inherited
Biological Process (BP) negative regulation of cellular catabolic process 0.01965 Highly Informative Inherited
Biological Process (BP) DNA damage checkpoint 0.02275 Highly Informative Inherited
Biological Process (BP) meiosis 0.4437 Highly Informative Inherited
Biological Process (BP) DNA recombination 0.3397 Highly Informative Inherited
Biological Process (BP) ossification 0.03853 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 0.01096 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 0.9924 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 0.0002834 Highly Informative Direct
Cellular Component (CC) protein complex 0.00000000002107 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 0.9498 Informative Inherited
Cellular Component (CC) cullin-RING ubiquitin ligase complex 0.00002849 Highly Informative Direct
Cellular Component (CC) neuromuscular junction 0.00000007299 Highly Informative Direct
Cellular Component (CC) microtubule organizing center part 0.0003651 Highly Informative Direct
Cellular Component (CC) centrosome 0.03272 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 phenotype0.3388Least InformativeInherited
Mammalian Phenotype (MP)digestive/alimentary phenotype0.1256Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system physiology0.352InformativeInherited
Mammalian Phenotype (MP)abnormal cell cycle0.004895Highly 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 cycle0.00001498Moderately InformativeDirect
Biological processBiological rhythms0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processNeurogenesis0.000000000006325InformativeDirect
Biological processMitosis0.00000000006471InformativeDirect
Biological processWnt signaling pathway0.000009169InformativeDirect
Biological processSporulation0.0003978InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCell junction0.0000000002563Moderately InformativeDirect
Cellular componentSynapse0.00004166InformativeDirect
Coding sequence diversityAlternative splicing0.000001113Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainLeucine-rich repeat0InformativeDirect
DomainWD repeat0InformativeDirect
DomainKelch repeat0Highly InformativeDirect
Post-translational modificationReceptor1Moderately InformativeInherited
Post-translational modificationGuanine-nucleotide releasing factor0.0002629InformativeDirect
Post-translational modificationPhotoreceptor protein0.000006721Highly InformativeDirect
Post-translational modificationUbl conjugation0.00006988Moderately 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 ]