SUPERFAMILY 1.75 HMM library and genome assignments server

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Ubiquitin-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   beta-Grasp (ubiquitin-like) [ 54235] (14)
Superfamily:   Ubiquitin-like [ 54236] (8)
Families:   Ubiquitin-related [ 54237] (38)
  UBX domain [ 54250] (5)
  GABARAP-like [ 54253] (3)
  First domain of FERM [ 54256] (6)
  Ras-binding domain, RBD [ 54263] (13)
  BM-002-like [ 75362] (3)
  APG12-like [ 142972]
  DIX domain [ 159926]


Superfamily statistics
Genomes (632) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 49,260 132,153 156
Proteins 41,531 112,843 155


Functional annotation
General category General
Detailed category General

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0.00000000000005609Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0.0102Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Omega peptidases0Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0.000000000004359Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.0000000004443Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep0.00003067Moderately InformativeDirect
Enzyme Commission (EC)Acting on the CH-CH group of donors0.00289Moderately InformativeInherited
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0.0000000000001949InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.00000366InformativeDirect
Enzyme Commission (EC)Phosphatidylinositol-4-phosphate 3-kinase0Highly InformativeDirect
Enzyme Commission (EC)Phosphatidylinositol-4,5-bisphosphate 3-kinase0Highly InformativeDirect
Enzyme Commission (EC)Phosphatidylinositol 3-kinase0.000000000612Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)cell type cancer0.5555Moderately InformativeInherited
Disease Ontology (DO)malignant glioma0.5741InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Somatic mutation0.0004828InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the head0.4308Least InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.1412Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the respiratory system0.3727Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology1Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.2448InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the dentition0.3721InformativeInherited
Phenotypic Abnormality (PA)Abnormal lung morphology0.5888InformativeInherited
Phenotypic Abnormality (PA)Abnormal tracheobronchial morphology0.2198Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)embryo phenotype0.2532Moderately InformativeInherited
Mammalian Phenotype (MP)neoplasm0.5116Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.0224InformativeInherited
Mammalian Phenotype (MP)increased hamartoma incidence0.000801Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell morphology variant0.0003729Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.001275Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.006513Least InformativeInherited
Worm Phenotype (WP)cell development variant0.01635Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.3739Least InformativeInherited
Worm Phenotype (WP)protein interaction variant0.00004565Moderately InformativeDirect
Worm Phenotype (WP)muscle cell physiology variant0.0002359InformativeDirect
Worm Phenotype (WP)epithelial system development variant0.1823InformativeInherited
Worm Phenotype (WP)body muscle dystrophy0.0000001518Highly InformativeDirect
Worm Phenotype (WP)gastrulation variant0.000139Highly InformativeDirect
Worm Phenotype (WP)cell polarity variant0.0005498Highly InformativeDirect
Worm Phenotype (WP)epithelial development variant0.006089Highly InformativeInherited
Worm Phenotype (WP)cell number decreased0.2244Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)metabolism and growth0.1854Least InformativeInherited
Yeast Phenotype (YP)protein/peptide accumulation0.0001303Highly InformativeDirect
Yeast Phenotype (YP)sexual cycle0.02105Highly InformativeInherited

Document: YP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)head0.0009265Least InformativeDirect
Xenopus ANatomical entity (XAN)nervous system0.00166Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.2455Least InformativeInherited
Xenopus ANatomical entity (XAN)brain0.0002655Moderately 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)pollen tube cell0.0000007609InformativeDirect
Plant ANatomical entity (PAN)gamete0.0005298InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage0.000003323Moderately InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0.0000000001648Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.0000000008392Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Aminoacyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)2.574e-16Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0.0000000002786Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.000000002276Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0.0000004051Moderately InformativeDirect
Enzyme Commission (EC)Omega peptidases0InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.000001851InformativeDirect
Enzyme Commission (EC)Protein-tyrosine kinases0.000008754InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00005231InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0.003827InformativeInherited
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0.000000000001552Highly InformativeDirect
Enzyme Commission (EC)Phosphoinositide phospholipase C0.00000001195Highly InformativeDirect

Document: EC annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 160 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 Ubiquitin-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 160 hidden Markov models representing the Ubiquitin-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 · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]