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 (536) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 20,667 21,908 68
Proteins 20,318 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 biogenesis0.005050.3116Least InformativeInherited
Biological Process (BP)biosynthetic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.79160.8049Least InformativeInherited
Biological Process (BP)single-organism cellular process0.95531Least 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)response to stimulus0.00073291Least InformativeInherited
Biological Process (BP)regulation of cellular process0.03771Least InformativeInherited
Biological Process (BP)cellular response to stress02.789e-12Moderately InformativeDirect
Biological Process (BP)cellular catabolic process4.344e-090Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process4.517e-060Moderately InformativeDirect
Biological Process (BP)cellular protein modification process1.644e-060.01784Moderately InformativeInherited
Biological Process (BP)regulation of protein metabolic process0.038551.366e-08Moderately InformativeInherited
Biological Process (BP)regulation of cellular component organization0.00011960.5569Moderately InformativeInherited
Biological Process (BP)regulation of developmental process0.01511Moderately InformativeInherited
Biological Process (BP)positive regulation of molecular function0.55990.193Moderately InformativeInherited
Biological Process (BP)regulation of catalytic activity10.5859Moderately InformativeInherited
Biological Process (BP)organelle organization0.044380.0003889Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.10550.1017Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process11Moderately InformativeInherited
Biological Process (BP)response to organic substance0.0003920.5165Moderately InformativeInherited
Biological Process (BP)positive regulation of metabolic process0.081760.6632Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process11Moderately InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.0029820.002588Moderately InformativeInherited
Biological Process (BP)proteolysis1.154e-090InformativeDirect
Biological Process (BP)response to DNA damage stimulus9.993e-077.203e-06InformativeDirect
Biological Process (BP)cell cycle process4.673e-083.755e-15InformativeDirect
Biological Process (BP)protein catabolic process00InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly1.42e-094.012e-11InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process00InformativeDirect
Biological Process (BP)positive regulation of protein metabolic process0.0001921.523e-05InformativeDirect
Biological Process (BP)protein modification by small protein conjugation or removal00InformativeDirect
Biological Process (BP)regulation of cellular catabolic process0.063450.4729InformativeInherited
Biological Process (BP)regulation of growth0.0064170.0495InformativeInherited
Biological Process (BP)regulation of anatomical structure morphogenesis0.083150.6018InformativeInherited
Biological Process (BP)mitotic cell cycle0.57720.004143InformativeInherited
Biological Process (BP)DNA metabolic process0.0016070.4689InformativeInherited
Biological Process (BP)regulation of protein ubiquitination9.803e-052.196e-10Highly InformativeDirect
Biological Process (BP)response to topologically incorrect protein4.893e-112.164e-12Highly InformativeDirect
Biological Process (BP)regulation of ligase activity5.28e-050Highly InformativeDirect
Biological Process (BP)regulation of proteolysis0.0011230.01971Highly InformativeInherited
Biological Process (BP)regulation of protein catabolic process8.276e-050.007733Highly InformativeInherited
Biological Process (BP)regulation of developmental growth5.856e-060.002561Highly InformativeInherited
Biological Process (BP)DNA replication0.00094150.1091Highly InformativeInherited
Biological Process (BP)protein polymerization0.057564.517e-07Highly InformativeInherited
Biological Process (BP)mitosis0.0021432.792e-10Highly InformativeInherited
Molecular Function (MF)binding0.00044981Least InformativeInherited
Molecular Function (MF)ligase activity00InformativeDirect
Molecular Function (MF)enzyme binding6.893e-070.0001584InformativeDirect
Molecular Function (MF)small conjugating protein ligase activity00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.65491Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)protein complex3.331e-060.09396Least InformativeInherited
Cellular Component (CC)nuclear part0.15450.5228Moderately InformativeInherited
Cellular Component (CC)ubiquitin ligase complex00InformativeDirect
Cellular Component (CC)nuclear ubiquitin ligase complex5.818e-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 0.3116 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) biosynthetic 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) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 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) regulation of metabolic process 0.8049 Least Informative Inherited
Biological Process (BP) organelle organization 0.0003889 Moderately Informative Direct
Biological Process (BP) cellular response to stress 2.789e-12 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 1.366e-08 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 cellular process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.01784 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.002588 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.5569 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.193 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.5859 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.1511 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.1017 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.5165 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.6632 Moderately Informative Inherited
Biological Process (BP) proteolysis 0 Informative Direct
Biological Process (BP) response to DNA damage stimulus 7.203e-06 Informative Direct
Biological Process (BP) cell cycle process 3.755e-15 Informative Direct
Biological Process (BP) protein catabolic process 0 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 4.012e-11 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0 Informative Direct
Biological Process (BP) positive regulation of protein metabolic process 1.523e-05 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.9453 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.4729 Informative Inherited
Biological Process (BP) regulation of growth 0.0495 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.6018 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.01382 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.198 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.003428 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.004143 Informative Inherited
Biological Process (BP) DNA metabolic process 0.4689 Informative Inherited
Biological Process (BP) regulation of translation 9.625e-05 Highly Informative Direct
Biological Process (BP) lysosome organization 4.828e-11 Highly Informative Direct
Biological Process (BP) mitosis 2.792e-10 Highly Informative Direct
Biological Process (BP) proteasomal protein catabolic process 0.0002045 Highly Informative Direct
Biological Process (BP) regulation of protein ubiquitination 2.196e-10 Highly Informative Direct
Biological Process (BP) response to topologically incorrect protein 2.164e-12 Highly Informative Direct
Biological Process (BP) protein polymerization 4.517e-07 Highly Informative Direct
Biological Process (BP) regulation of ligase activity 0 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.01934 Highly Informative Inherited
Biological Process (BP) protein ubiquitination 1 Highly Informative Inherited
Biological Process (BP) regulation of proteolysis 0.01971 Highly Informative Inherited
Biological Process (BP) regulation of protein catabolic process 0.007733 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 0.002561 Highly Informative Inherited
Biological Process (BP) DNA replication 0.1091 Highly Informative Inherited
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 0.008551 Highly Informative Inherited
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.7254 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 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 0.0001584 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) small conjugating protein ligase activity 0 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.8765 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 0.09396 Least Informative Inherited
Cellular Component (CC) organelle membrane 0.9008 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.5228 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 0 Informative Direct
Cellular Component (CC) endosome 0.004853 Informative Inherited
Cellular Component (CC) nuclear ubiquitin ligase complex 0 Highly Informative Direct
Cellular Component (CC) endosomal part 5.43e-07 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)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 cell2.3e-05InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage1.184e-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--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 cycle2.169e-13Moderately InformativeDirect
Biological processApoptosis2.189e-12Moderately InformativeDirect
Biological processProtein transport3.238e-07Moderately InformativeDirect
Biological processDNA damage2.018e-05Moderately InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processSporulation2.372e-16InformativeDirect
Biological processTranslation regulation2.549e-06InformativeDirect
Biological processGrowth regulation5.551e-06Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentEndosome3.533e-09Moderately 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 regulator1.007e-10InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond7.258e-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 ]