SUPERFAMILY 1.75 HMM library and genome assignments server

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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 system0.009043Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.03034Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.1172Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.3598Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.9139Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.004989Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.05052Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal globe morphology0.1058Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal muscle tone0.6789Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa morphology0.8048Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the uvea0.04593InformativeInherited
Phenotypic Abnormality (PA)Abnormal retinal morphology0.1891InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lipid metabolism0.2301InformativeInherited
Phenotypic Abnormality (PA)Muscular hypotonia0.5753InformativeInherited
Phenotypic Abnormality (PA)Abnormal chorioretinal morphology0.005971Highly InformativeInherited
Phenotypic Abnormality (PA)Precocious puberty0.04984Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.3928Least InformativeInherited
Mammalian Phenotype (MP)neoplasm0.00967Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.3512Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.4464Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.7524Moderately InformativeInherited
Mammalian Phenotype (MP)chromosomal instability0.0006884InformativeDirect
Mammalian Phenotype (MP)abnormal intestine morphology0.5925InformativeInherited
Mammalian Phenotype (MP)abnormal hypaxial muscle morphology0.6914InformativeInherited
Mammalian Phenotype (MP)abnormal small intestine morphology0.04747Highly InformativeInherited
Mammalian Phenotype (MP)abnormal crypts of Lieberkuhn morphology0.3561Highly 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 variant8.875e-16Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.8218Least InformativeInherited
Worm Phenotype (WP)protein protein interaction variant0Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.00000000002054Moderately InformativeDirect
Worm Phenotype (WP)cell homeostasis metabolism variant0.007965Moderately InformativeInherited
Worm Phenotype (WP)neuron migration variant0InformativeDirect
Worm Phenotype (WP)cell stress response variant0.000005484InformativeDirect
Worm Phenotype (WP)germ cell ionizing radiation response variant0.5604Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)embryo0.4195Least InformativeInherited
Fly Anatomy (FA)larva0.4566Least InformativeInherited
Fly Anatomy (FA)somatic cell0.8767Least InformativeInherited
Fly Anatomy (FA)late embryo0.6808Moderately InformativeInherited
Fly Anatomy (FA)embryonic/larval circulatory system0.1869InformativeInherited
Fly Anatomy (FA)embryonic/larval garland cell0.0001307Highly InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA 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)leaf0.6305Least InformativeInherited
Plant ANatomical entity (PAN)pollen tube cell0.00008752InformativeDirect
Plant ANatomical entity (PAN)leaf epidermis0.0001955Highly InformativeDirect
Plant ANatomical entity (PAN)trichome0.00572Highly InformativeInherited
Plant structure DEvelopment stage (PDE)pollen development stage0.000009811Moderately 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)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)0.002112Moderately InformativeInherited
Enzyme Commission (EC)Glycosyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0InformativeDirect
Enzyme Commission (EC)Omega peptidases0InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0.0000000000008192InformativeDirect
Enzyme Commission (EC)Hexosyltransferases0.4817InformativeInherited

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) · 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 27 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 27 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) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]