SUPERFAMILY 1.75 HMM library and genome assignments server

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 (537) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 20,737 21,908 68
Proteins 20,386 21,526 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 biogenesis0.0034570.2195Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)biosynthetic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.77340.8589Least InformativeInherited
Biological Process (BP)positive regulation of biological process11Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)single-organism metabolic process11Least InformativeInherited
Biological Process (BP)response to stimulus0.00043571Least InformativeInherited
Biological Process (BP)regulation of cellular process0.074931Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)cellular response to stress00.000000000005302Moderately InformativeDirect
Biological Process (BP)cellular catabolic process0.0000000034140Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process0.0000032320Moderately InformativeDirect
Biological Process (BP)regulation of protein metabolic process0.081950.0000000306Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.12490.289Moderately InformativeInherited
Biological Process (BP)regulation of developmental process0.015091Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process11Moderately InformativeInherited
Biological Process (BP)positive regulation of molecular function0.58840.2072Moderately InformativeInherited
Biological Process (BP)regulation of catalytic activity10.6274Moderately InformativeInherited
Biological Process (BP)positive regulation of metabolic process0.34311Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process11Moderately InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.000027650.01625Moderately InformativeInherited
Biological Process (BP)response to organic substance0.00054440.5633Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.0000017050.01684Moderately InformativeInherited
Biological Process (BP)single-organism organelle organization0.0000029840.001116Moderately InformativeInherited
Biological Process (BP)regulation of cellular component organization0.00023730.691Moderately InformativeInherited
Biological Process (BP)DNA repair00InformativeDirect
Biological Process (BP)proteolysis0.0000000007380InformativeDirect
Biological Process (BP)cell cycle process0.0000000000011420InformativeDirect
Biological Process (BP)protein catabolic process00InformativeDirect
Biological Process (BP)positive regulation of cellular protein metabolic process0.00033760.00000498InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly0.0000000023160.000000000116InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process00InformativeDirect
Biological Process (BP)organelle fission0.000015420.00000000002721InformativeDirect
Biological Process (BP)cell division0.0000018910.0000000001879InformativeDirect
Biological Process (BP)protein modification by small protein conjugation or removal00InformativeDirect
Biological Process (BP)regulation of growth0.0053330.04782InformativeInherited
Biological Process (BP)regulation of anatomical structure morphogenesis0.077860.6062InformativeInherited
Biological Process (BP)regulation of transferase activity0.092710.002318InformativeInherited
Biological Process (BP)regulation of cellular catabolic process0.0079490.1927InformativeInherited
Biological Process (BP)mitotic cell cycle0.65230.02964InformativeInherited
Biological Process (BP)nuclear division0.00040580.000001092Highly InformativeDirect
Biological Process (BP)response to topologically incorrect protein0.000000000049910.000000000002597Highly InformativeDirect
Biological Process (BP)regulation of ligase activity0.000056860Highly InformativeDirect
Biological Process (BP)regulation of proteolysis involved in cellular protein catabolic process0.000000013250.00000611Highly InformativeDirect
Biological Process (BP)positive regulation of protein modification by small protein conjugation or removal0.000000085670Highly InformativeDirect
Biological Process (BP)regulation of developmental growth0.0000060070.002858Highly InformativeInherited
Biological Process (BP)regulation of protein ubiquitination0.90891Highly InformativeInherited
Biological Process (BP)DNA replication0.001150.123Highly InformativeInherited
Biological Process (BP)protein polymerization0.075530.00001065Highly InformativeInherited
Molecular Function (MF)transferase activity00Least InformativeDirect
Molecular Function (MF)binding0.0010641Least InformativeInherited
Molecular Function (MF)ligase activity00InformativeDirect
Molecular Function (MF)enzyme binding0.0000000050.00001137InformativeDirect
Molecular Function (MF)ubiquitin-protein transferase activity00Highly InformativeDirect
Molecular Function (MF)acid-amino acid ligase activity00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.63011Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)protein complex0.036270.1437Least InformativeInherited
Cellular Component (CC)transferase complex0.0000000010910.0000000001248Moderately InformativeDirect
Cellular Component (CC)nuclear part0.12540.3589Moderately InformativeInherited
Cellular Component (CC)ubiquitin ligase complex00InformativeDirect
Cellular Component (CC)nuclear ubiquitin ligase complex0.0000066090Highly InformativeDirect

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) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.2195 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.8589 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular response to stress 0.000000000005302 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.0000000306 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0 Moderately Informative Direct
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) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.2072 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.6274 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.01625 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.1921 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.01684 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.5633 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.001116 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.289 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.691 Moderately Informative Inherited
Biological Process (BP) DNA repair 0 Informative Direct
Biological Process (BP) proteolysis 0 Informative Direct
Biological Process (BP) cell cycle process 0 Informative Direct
Biological Process (BP) protein catabolic process 0 Informative Direct
Biological Process (BP) positive regulation of cellular protein metabolic process 0.00000498 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.000000000116 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0 Informative Direct
Biological Process (BP) organelle fission 0.00000000002721 Informative Direct
Biological Process (BP) cell division 0.0000000001879 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.00006157 Informative Direct
Biological Process (BP) regulation of growth 0.04782 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.6062 Informative Inherited
Biological Process (BP) regulation of transferase activity 0.002318 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.07479 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.1927 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.02695 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.02964 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.003926 Informative Inherited
Biological Process (BP) nuclear division 0.000001092 Highly Informative Direct
Biological Process (BP) regulation of translation 0.0001154 Highly Informative Direct
Biological Process (BP) lysosome organization 0.00000000005448 Highly Informative Direct
Biological Process (BP) proteasomal protein catabolic process 0.0004129 Highly Informative Direct
Biological Process (BP) response to topologically incorrect protein 0.000000000002597 Highly Informative Direct
Biological Process (BP) protein polymerization 0.00001065 Highly Informative Direct
Biological Process (BP) regulation of ligase activity 0 Highly Informative Direct
Biological Process (BP) regulation of proteolysis involved in cellular protein catabolic process 0.00000611 Highly Informative Direct
Biological Process (BP) positive regulation of protein modification by small protein conjugation or removal 0 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0249 Highly Informative Inherited
Biological Process (BP) protein ubiquitination 1 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 0.002858 Highly Informative Inherited
Biological Process (BP) regulation of protein ubiquitination 1 Highly Informative Inherited
Biological Process (BP) DNA replication 0.123 Highly Informative Inherited
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 0.001658 Highly Informative Inherited
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.7388 Highly Informative Inherited
Molecular Function (MF) transferase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) enzyme binding 0.00001137 Informative Direct
Molecular Function (MF) kinase activity 1 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 1 Informative Inherited
Molecular Function (MF) ubiquitin-protein transferase activity 0 Highly Informative Direct
Molecular Function (MF) acid-amino acid ligase activity 0 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.8945 Highly Informative Inherited
Cellular Component (CC) protein complex 0.1437 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 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) transferase complex 0.0000000001248 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0.3612 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.3589 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 0 Informative Direct
Cellular Component (CC) endosome 0.005604 Informative Inherited
Cellular Component (CC) nuclear ubiquitin ligase complex 0 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0000006343 Highly Informative Direct

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 variant0.000000004857Least InformativeDirect
Worm Phenotype (WP)protein aggregation variant0Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.000000000000006724Moderately 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)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0.002163Least InformativeInherited
Xenopus ANatomical entity (XAN)gamete0.0003333Moderately 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)sporangium0.0003729Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0.01638Least InformativeInherited
Plant ANatomical entity (PAN)microsporophyll0.07285Least InformativeInherited
Plant ANatomical entity (PAN)pollen tube cell0.000023InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage0.00000001184Moderately 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--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 cycle0.0000000000002169Moderately InformativeDirect
Biological processApoptosis0.000000000002189Moderately InformativeDirect
Biological processProtein transport0.0000003238Moderately InformativeDirect
Biological processDNA damage0.00002018Moderately InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processSporulation2.372e-16InformativeDirect
Biological processTranslation regulation0.000002549InformativeDirect
Biological processGrowth regulation0.000005551Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentEndosome0.000000003533Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.0005701Moderately InformativeDirect
Coding sequence diversityAlternative splicing0.0006516Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationChromatin regulator0.0000000001007InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0.00007258Moderately 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 ]