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UBC-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   UBC-like [ 54494]
Superfamily:   UBC-like [ 54495] (4)
Families:   UBC-related [ 54496] (6)
  UEV domain [ 75383] (2)
  RWD domain [ 110843] (4)
  UFC1-like [ 143072]

 Superfamily statistics
Genomes (469) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 18,506 15,289 68
Proteins 18,241 15,063 68

 Functional annotation
General category Processes_IC
Detailed category Protein modification

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)protein metabolic process00Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process00Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.0017640.07392Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)biosynthetic process11Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.81770.7064Least InformativeInherited
Biological Process (BP)single-organism cellular process0.731Least InformativeInherited
Biological Process (BP)response to stimulus4.64e-051Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)regulation of cellular process0.039941Least InformativeInherited
Biological Process (BP)cellular response to stress2.095e-133.352e-13Moderately InformativeDirect
Biological Process (BP)cellular catabolic process2.389e-100Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process2.864e-070Moderately InformativeDirect
Biological Process (BP)cellular response to chemical stimulus11Moderately InformativeInherited
Biological Process (BP)response to organic substance0.00015370.1695Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.0015070.1745Moderately InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.0016020.0009117Moderately InformativeInherited
Biological Process (BP)regulation of protein metabolic process0.07915.398e-08Moderately InformativeInherited
Biological Process (BP)regulation of cellular component organization0.00068910.2501Moderately InformativeInherited
Biological Process (BP)regulation of molecular function10.2845Moderately InformativeInherited
Biological Process (BP)regulation of developmental process0.024880.9905Moderately InformativeInherited
Biological Process (BP)organelle organization0.031110.0001027Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.12150.1254Moderately InformativeInherited
Biological Process (BP)positive regulation of metabolic process0.067660.7846Moderately InformativeInherited
Biological Process (BP)regulation of cellular metabolic process0.35230.2814Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process11Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process11Moderately InformativeInherited
Biological Process (BP)proteolysis7.444e-120InformativeDirect
Biological Process (BP)response to DNA damage stimulus3.979e-081.495e-06InformativeDirect
Biological Process (BP)cell cycle process2.87e-080InformativeDirect
Biological Process (BP)protein catabolic process00InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly2.318e-115.957e-13InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process00InformativeDirect
Biological Process (BP)positive regulation of protein metabolic process0.00021140.0006722InformativeDirect
Biological Process (BP)protein modification by small protein conjugation or removal00InformativeDirect
Biological Process (BP)regulation of cellular catabolic process0.068550.1638InformativeInherited
Biological Process (BP)regulation of anatomical structure morphogenesis0.0460.2795InformativeInherited
Biological Process (BP)positive regulation of catalytic activity0.20660.032InformativeInherited
Biological Process (BP)regulation of growth0.010930.02425InformativeInherited
Biological Process (BP)DNA metabolic process0.0016480.274InformativeInherited
Biological Process (BP)nuclear division1.632e-080Highly InformativeDirect
Biological Process (BP)DNA repair8.326e-085.233e-08Highly InformativeDirect
Biological Process (BP)modification-dependent protein catabolic process00Highly InformativeDirect
Biological Process (BP)regulation of protein ubiquitination0.0001881.471e-12Highly InformativeDirect
Biological Process (BP)response to topologically incorrect protein3.01e-112.684e-12Highly InformativeDirect
Biological Process (BP)regulation of developmental growth2.491e-060.0006511Highly InformativeDirect
Biological Process (BP)regulation of ligase activity4.543e-050Highly InformativeDirect
Biological Process (BP)regulation of proteolysis0.033150.05648Highly InformativeInherited
Biological Process (BP)regulation of protein catabolic process0.00039530.007494Highly InformativeInherited
Biological Process (BP)regulation of cell morphogenesis0.013560.1276Highly InformativeInherited
Biological Process (BP)DNA replication0.0025150.1249Highly InformativeInherited
Biological Process (BP)protein polymerization0.10048.163e-08Highly InformativeInherited
Molecular Function (MF)binding0.034241Least InformativeInherited
Molecular Function (MF)protein binding4.297e-070.7595Moderately InformativeInherited
Molecular Function (MF)ligase activity, forming carbon-nitrogen bonds00InformativeDirect
Molecular Function (MF)enzyme binding0.024630.1185InformativeInherited
Molecular Function (MF)small conjugating protein ligase activity00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.60011Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)protein complex2.299e-050.1049Least InformativeInherited
Cellular Component (CC)nuclear part0.14140.3075Moderately InformativeInherited
Cellular Component (CC)ubiquitin ligase complex00InformativeDirect
Cellular Component (CC)nuclear ubiquitin ligase complex5.757e-060Highly InformativeDirect
Cellular Component (CC)cullin-RING ubiquitin ligase complex11Highly 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 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.07392 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.7064 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organelle organization 0.0001027 Moderately Informative Direct
Biological Process (BP) cellular response to stress 3.352e-13 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.0009117 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 5.398e-08 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.1695 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.2501 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.2845 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.9905 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.1254 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.7846 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 0.2814 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.4364 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.1745 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 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) response to DNA damage stimulus 1.495e-06 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.0006674 Informative Direct
Biological Process (BP) cytoplasmic transport 0.0002298 Informative Direct
Biological Process (BP) cell cycle process 0 Informative Direct
Biological Process (BP) protein catabolic process 0 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 5.957e-13 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0 Informative Direct
Biological Process (BP) positive regulation of protein metabolic process 0.0006722 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0.1638 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.2795 Informative Inherited
Biological Process (BP) positive regulation of catalytic activity 0.032 Informative Inherited
Biological Process (BP) regulation of growth 0.02425 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.2122 Informative Inherited
Biological Process (BP) DNA metabolic process 0.274 Informative Inherited
Biological Process (BP) nuclear division 0 Highly Informative Direct
Biological Process (BP) DNA repair 5.233e-08 Highly Informative Direct
Biological Process (BP) regulation of translation 1.18e-05 Highly Informative Direct
Biological Process (BP) lysosome organization 3.077e-11 Highly Informative Direct
Biological Process (BP) proteasomal protein catabolic process 9.985e-05 Highly Informative Direct
Biological Process (BP) endosomal transport 3.587e-12 Highly Informative Direct
Biological Process (BP) modification-dependent protein catabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of protein ubiquitination 1.471e-12 Highly Informative Direct
Biological Process (BP) response to topologically incorrect protein 2.684e-12 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 0.0006511 Highly Informative Direct
Biological Process (BP) protein polymerization 8.163e-08 Highly Informative Direct
Biological Process (BP) regulation of ligase activity 0 Highly Informative Direct
Biological Process (BP) protein ubiquitination 1 Highly Informative Inherited
Biological Process (BP) regulation of proteolysis 0.05648 Highly Informative Inherited
Biological Process (BP) regulation of protein catabolic process 0.007494 Highly Informative Inherited
Biological Process (BP) regulation of cell morphogenesis 0.1276 Highly Informative Inherited
Biological Process (BP) DNA replication 0.1249 Highly Informative Inherited
Biological Process (BP) protein glycosylation 1 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) protein binding 0.7595 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 0 Informative Direct
Molecular Function (MF) enzyme binding 0.1185 Informative Inherited
Molecular Function (MF) kinase activity 1 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.9941 Informative Inherited
Molecular Function (MF) small conjugating protein ligase activity 0 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.7942 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.1049 Least Informative Inherited
Cellular Component (CC) organelle membrane 0.865 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.3075 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 0 Informative Direct
Cellular Component (CC) endosome 0.005354 Informative Inherited
Cellular Component (CC) nuclear ubiquitin ligase complex 0 Highly Informative Direct
Cellular Component (CC) endosomal part 4.119e-06 Highly Informative Direct
Cellular Component (CC) cullin-RING ubiquitin ligase complex 1 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Forming carbon-nitrogen bonds0Moderately InformativeDirect
Enzyme Commission (EC)Acid--D-amino-acid ligases (peptide synthases)0InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant4.857e-09Least InformativeDirect
Worm Phenotype (WP)protein aggregation variant0Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant6.724e-15Moderately InformativeDirect
Worm Phenotype (WP)organism segment morphology variant0.2518Moderately InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)male genitalia0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0.001772Least InformativeInherited
Xenopus ANatomical entity (XAN)gamete0.0003354Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)sporangium7.3e-05Least InformativeDirect
Plant ANatomical entity (PAN)plant cell0.00281Least InformativeInherited
Plant ANatomical entity (PAN)microgametophyte0.006838Least InformativeInherited
Plant ANatomical entity (PAN)microsporophyll0.03299Least InformativeInherited
Plant ANatomical entity (PAN)pollen tube cell0.0002956InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage1.397e-08Moderately InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Acid--D-amino-acid ligases (peptide synthases)0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processCell cycle2.673e-13Moderately InformativeDirect
Biological processApoptosis1.289e-12Moderately InformativeDirect
Biological processProtein transport2.052e-07Moderately InformativeDirect
Biological processDNA damage2.206e-05Moderately InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processSporulation2.336e-16InformativeDirect
Biological processTranslation regulation2.267e-06InformativeDirect
Biological processGrowth regulation2.495e-06Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentEndosome6.822e-10Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.0003444Moderately InformativeDirect
Coding sequence diversityAlternative splicing0.0004364Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationChromatin regulator6.303e-11InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond1.399e-05Moderately InformativeDirect
Post-translational modificationAcetylation1.864e-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) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · 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 42 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 UBC-like 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 42 hidden Markov models representing the UBC-like 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) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

Please send feedback, comments or questions to superfamily@cs.bris.ac.uk or use the feedback form.

© Copyright 2013 The SUPERFAMILY authors and Julian Gough.