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.


RING/U-box superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   RING/U-box [ 57849]
Superfamily:   RING/U-box [ 57850] (6)
Families:   RING finger domain, C3HC4 [ 57851] (14)
  U-box [ 90222] (4)
  Variant RING domain [ 118300] (2)
  IBR domain [ 144228]
  Zf-UBP [ 161204] (3)
  ZZ domain [ 161211] (3)


Superfamily statistics
Genomes (697) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 115,075 298,266 32
Proteins 102,869 266,696 32


Functional annotation
General category Information
Detailed category DNA replication/repair

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)0Least InformativeDirect
Enzyme Commission (EC)Isomerases0.0228Least InformativeInherited
Enzyme Commission (EC)Omega peptidases0Moderately InformativeDirect
Enzyme Commission (EC)Glycosyltransferases0.000000001652Moderately InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0.000004836Moderately InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0InformativeDirect
Enzyme Commission (EC)Peptidylprolyl isomerase0.0000000000006579InformativeDirect
Enzyme Commission (EC)Cellulose synthase (UDP-forming)0Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.0243Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.0859Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.1518Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.6903Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.007153Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal posterior eye segment morphology0.5543Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa morphology0.6922Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal circulating metabolite concentration0.873Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal uvea morphology0.0548InformativeInherited
Phenotypic Abnormality (PA)Congenital abnormal hair pattern0.09368InformativeInherited
Phenotypic Abnormality (PA)Abnormal circulating lipid concentration0.2703InformativeInherited
Phenotypic Abnormality (PA)Abnormal retinal morphology0.2907InformativeInherited
Phenotypic Abnormality (PA)Abnormal circulating fatty-acid concentration0.01652Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal choroid morphology0.03193Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormality of female external genitalia0.0882Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.3893Least InformativeInherited
Mammalian Phenotype (MP)neoplasm0.009593Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.3485Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.4471Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.7513Moderately InformativeInherited
Mammalian Phenotype (MP)chromosomal instability0.0006846InformativeDirect
Mammalian Phenotype (MP)abnormal intestine morphology0.5919InformativeInherited
Mammalian Phenotype (MP)abnormal hypaxial muscle morphology0.6891InformativeInherited
Mammalian Phenotype (MP)abnormal small intestine morphology0.04736Highly InformativeInherited
Mammalian Phenotype (MP)abnormal crypts of Lieberkuhn morphology0.3574Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell development variant0Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.000000000000286Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.4159Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.6204Least InformativeInherited
Worm Phenotype (WP)protein interaction variant0Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.00000000004926Moderately InformativeDirect
Worm Phenotype (WP)cell homeostasis metabolism variant0.004685Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.1053Moderately InformativeInherited
Worm Phenotype (WP)neuron migration variant0InformativeDirect
Worm Phenotype (WP)organism ionizing radiation response variant0.00000001061InformativeDirect
Worm Phenotype (WP)cell stress response variant0.0000003666InformativeDirect
Worm Phenotype (WP)germ cell ionizing radiation response variant0.000000005814Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)cell0.1086Least InformativeInherited
Fly Anatomy (FA)larva0.5796Least InformativeInherited
Fly Anatomy (FA)embryo0.4698Moderately InformativeInherited
Fly Anatomy (FA)embryonic/larval circulatory system0.196InformativeInherited
Fly Anatomy (FA)nephrocyte0.05289Highly InformativeInherited

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)leaf0.6301Least InformativeInherited
Plant ANatomical entity (PAN)pollen tube cell0.00008872InformativeDirect
Plant ANatomical entity (PAN)leaf epidermis0.0001964Highly InformativeDirect
Plant ANatomical entity (PAN)trichome0.005743Highly InformativeInherited
Plant structure DEvelopment stage (PDE)pollen development stage0.000009929Moderately InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Aminoacyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)0.004376Moderately InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups1Moderately InformativeInherited
Enzyme Commission (EC)Glycosyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0InformativeDirect
Enzyme Commission (EC)Omega peptidases0InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0.0000000000006198InformativeDirect
Enzyme Commission (EC)Hexosyltransferases0.5652InformativeInherited

Document: EC annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Anatomy (FA) · 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 38 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 RING/U-box 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 38 hidden Markov models representing the RING/U-box 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) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]