SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 cancer0.5566Moderately InformativeInherited
Disease Ontology (DO)malignant glioma0.5743InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Somatic mutation0.00006498InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the head0.8353Least InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.07706Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the respiratory system0.5285Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology1Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.1927InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the dentition0.4501InformativeInherited
Phenotypic Abnormality (PA)Abnormal lung morphology0.5984InformativeInherited
Phenotypic Abnormality (PA)Abnormal tracheobronchial morphology0.2142Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)embryo phenotype0.2522Moderately InformativeInherited
Mammalian Phenotype (MP)neoplasm0.5118Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.02254InformativeInherited
Mammalian Phenotype (MP)increased hamartoma incidence0.0008037Highly 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 variant0.0001265Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.0002733Least InformativeDirect
Worm Phenotype (WP)cell development variant0.02041Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.5223Least InformativeInherited
Worm Phenotype (WP)protein protein interaction variant0.0000001515Moderately InformativeDirect
Worm Phenotype (WP)cell number increased0.007348InformativeInherited
Worm Phenotype (WP)epithelial system development variant0.1327InformativeInherited
Worm Phenotype (WP)body muscle dystrophy0.00000008081Highly InformativeDirect
Worm Phenotype (WP)cell polarity variant0.0003835Highly InformativeDirect
Worm Phenotype (WP)epithelial development variant0.005534Highly InformativeInherited
Worm Phenotype (WP)cell number decreased0.1299Highly 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)head0.0008675Least InformativeDirect
Xenopus ANatomical entity (XAN)cavitated compound organ0.2435Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)brain0.000554Moderately 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 groups0.000000000161Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.00000000131Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Aminoacyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)0Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0.0000000002421Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.000000001675Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0.0000004018Moderately InformativeDirect
Enzyme Commission (EC)Omega peptidases0InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.000001942InformativeDirect
Enzyme Commission (EC)Protein-tyrosine kinases0.000008494InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00005223InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0.01894InformativeInherited
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0.000000000001571Highly InformativeDirect
Enzyme Commission (EC)Phosphoinositide phospholipase C0.00000001201Highly 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 ]