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 biogenesis0.0046540.2932Least InformativeInherited
Biological Process (BP)biosynthetic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.79680.7788Least InformativeInherited
Biological Process (BP)single-organism cellular process0.9551Least 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 stimulus0.00068371Least InformativeInherited
Biological Process (BP)regulation of cellular process0.036281Least InformativeInherited
Biological Process (BP)cellular response to stress02.038e-12Moderately InformativeDirect
Biological Process (BP)cellular catabolic process3.34e-090Moderately InformativeDirect
Biological Process (BP)cellular protein modification process1.737e-060.01762Moderately InformativeInherited
Biological Process (BP)regulation of protein metabolic process0.035831.096e-08Moderately InformativeInherited
Biological Process (BP)regulation of cellular component organization0.0001050.5386Moderately InformativeInherited
Biological Process (BP)regulation of developmental process0.013541Moderately InformativeInherited
Biological Process (BP)positive regulation of molecular function0.58290.2167Moderately InformativeInherited
Biological Process (BP)regulation of catalytic activity10.5912Moderately InformativeInherited
Biological Process (BP)organelle organization0.043870.0003709Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.10520.0983Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process11Moderately InformativeInherited
Biological Process (BP)response to organic substance0.0003560.5004Moderately InformativeInherited
Biological Process (BP)positive regulation of metabolic process0.073880.6328Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process11Moderately InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.0030810.002436Moderately InformativeInherited
Biological Process (BP)proteolysis1.047e-090InformativeDirect
Biological Process (BP)response to DNA damage stimulus1.082e-068.466e-06InformativeDirect
Biological Process (BP)cell cycle process4.974e-083.741e-15InformativeDirect
Biological Process (BP)protein catabolic process00InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly1.389e-093.119e-11InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process00InformativeDirect
Biological Process (BP)protein modification by small protein conjugation or removal00InformativeDirect
Biological Process (BP)regulation of cellular catabolic process0.076060.4894InformativeInherited
Biological Process (BP)regulation of growth0.006650.04738InformativeInherited
Biological Process (BP)regulation of anatomical structure morphogenesis0.07960.589InformativeInherited
Biological Process (BP)positive regulation of protein modification process0.56770.004528InformativeInherited
Biological Process (BP)mitotic cell cycle0.57020.004116InformativeInherited
Biological Process (BP)DNA metabolic process0.0016610.4748InformativeInherited
Biological Process (BP)regulation of protein ubiquitination0.00010022.195e-10Highly InformativeDirect
Biological Process (BP)response to topologically incorrect protein5.292e-112.427e-12Highly InformativeDirect
Biological Process (BP)regulation of ligase activity5.297e-050Highly InformativeDirect
Biological Process (BP)regulation of proteolysis0.0011570.02005Highly InformativeInherited
Biological Process (BP)regulation of protein catabolic process7.789e-050.007536Highly InformativeInherited
Biological Process (BP)regulation of developmental growth5.734e-060.002484Highly InformativeInherited
Biological Process (BP)DNA replication0.0019990.1443Highly InformativeInherited
Biological Process (BP)protein polymerization0.05754.784e-07Highly InformativeInherited
Biological Process (BP)mitosis0.0021163.046e-10Highly InformativeInherited
Molecular Function (MF)binding0.00042911Least InformativeInherited
Molecular Function (MF)ligase activity, forming carbon-nitrogen bonds00InformativeDirect
Molecular Function (MF)enzyme binding6.989e-070.0001463InformativeDirect
Molecular Function (MF)small conjugating protein ligase activity00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.64851Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)protein complex3.314e-060.09108Least InformativeInherited
Cellular Component (CC)nuclear part0.15560.5243Moderately InformativeInherited
Cellular Component (CC)ubiquitin ligase complex00InformativeDirect
Cellular Component (CC)nuclear ubiquitin ligase complex5.906e-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 0.2932 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 0.7788 Least Informative Inherited
Biological Process (BP) organelle organization 0.0003709 Moderately Informative Direct
Biological Process (BP) cellular response to stress 2.038e-12 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 1.096e-08 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 0.01762 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.002436 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.5386 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.2167 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.5912 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 0.1464 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.0983 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 0.5004 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.6328 Moderately Informative Inherited
Biological Process (BP) proteolysis 0 Informative Direct
Biological Process (BP) response to DNA damage stimulus 8.466e-06 Informative Direct
Biological Process (BP) cell cycle process 3.741e-15 Informative Direct
Biological Process (BP) protein catabolic process 0 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 3.119e-11 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.9392 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.4894 Informative Inherited
Biological Process (BP) regulation of growth 0.04738 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.589 Informative Inherited
Biological Process (BP) positive regulation of protein modification process 0.004528 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.01397 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.1957 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.003393 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.004116 Informative Inherited
Biological Process (BP) DNA metabolic process 0.4748 Informative Inherited
Biological Process (BP) regulation of translation 0.0001049 Highly Informative Direct
Biological Process (BP) lysosome organization 4.899e-11 Highly Informative Direct
Biological Process (BP) mitosis 3.046e-10 Highly Informative Direct
Biological Process (BP) proteasomal protein catabolic process 0.0001923 Highly Informative Direct
Biological Process (BP) regulation of protein ubiquitination 2.195e-10 Highly Informative Direct
Biological Process (BP) response to topologically incorrect protein 2.427e-12 Highly Informative Direct
Biological Process (BP) protein polymerization 4.784e-07 Highly Informative Direct
Biological Process (BP) regulation of ligase activity 0 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.01788 Highly Informative Inherited
Biological Process (BP) protein ubiquitination 1 Highly Informative Inherited
Biological Process (BP) regulation of proteolysis 0.02005 Highly Informative Inherited
Biological Process (BP) regulation of protein catabolic process 0.007536 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 0.002484 Highly Informative Inherited
Biological Process (BP) DNA replication 0.1443 Highly Informative Inherited
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 0.008645 Highly Informative Inherited
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.7243 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, forming carbon-nitrogen bonds 0 Informative Direct
Molecular Function (MF) enzyme binding 0.0001463 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 0.8821 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 0.09108 Least Informative Inherited
Cellular Component (CC) organelle membrane 0.8961 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.5243 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 0 Informative Direct
Cellular Component (CC) endosome 0.004779 Informative Inherited
Cellular Component (CC) nuclear ubiquitin ligase complex 0 Highly Informative Direct
Cellular Component (CC) endosomal part 5.628e-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
Yeast Phenotype (YP)thermotolerance0.0003811Highly 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)cell0.002119Least InformativeInherited
Xenopus ANatomical entity (XAN)gamete0.0003308Moderately 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 cycle2.506e-13Moderately InformativeDirect
Biological processApoptosis1.926e-12Moderately InformativeDirect
Biological processProtein transport2.827e-07Moderately InformativeDirect
Biological processDNA damage1.779e-05Moderately InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processSporulation2.37e-16InformativeDirect
Biological processTranslation regulation2.353e-06InformativeDirect
Biological processGrowth regulation5.371e-06Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentEndosome2.901e-09Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.0004891Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationChromatin regulator7.983e-11InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond6.786e-05Moderately InformativeDirect

Document: KW 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) ]

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) · Internal database links ]