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Restriction endonuclease-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Restriction endonuclease-like [ 52979] (4)
Superfamily:   Restriction endonuclease-like [ 52980] (33)
Families:   Restriction endonuclease EcoRI [ 52981]
  Restriction endonuclease EcoRV [ 52984]
  Restriction endonuclease BamHI [ 52987]
  Restriction endonuclease BglI [ 52990]
  Restriction endonuclease BglII [ 52993]
  Restriction endonuclease BstyI [ 102471]
  Restriction endonuclease PvuII [ 52996]
  Cfr10I/Bse634I [ 52999] (2)
  Restriction endonuclease MunI [ 53002]
  Restriction endonuclease NaeI [ 53005]
  Restriction endonuclease NgoIV [ 53008]
  Restriction endonuclease BsobI [ 53011]
  Restriction endonuclease HincII [ 69525]
  Restriction endonuclease FokI, C-terminal (catalytic) domain [ 53014]
  Type II restriction endonuclease catalytic domain [ 102474]
  lambda exonuclease [ 53017]
  DNA mismatch repair protein MutH from [ 53020]
  Very short patch repair (VSR) endonuclease [ 53023]
  TnsA endonuclease, N-terminal domain [ 53026]
  Endonuclease I (Holliday junction resolvase) [ 53029]
  Hjc-like [ 64080] (2)
  XPF/Rad1/Mus81 nuclease [ 89716] (3)
  Restriction endonuclease MspI [ 110624]
  Exodeoxyribonuclease V beta chain (RecB), C-terminal domain [ 117619]
  Exodeoxyribonuclease V beta chain (RecC), C-terminal domain [ 117622]
  Hypothetical protein VC1899 [ 117625]
  Hypothetical protein TT1808 (TTHA1514) [ 117628]
  RecU-like [ 117631]
  Restriction endonuclease EcoO109IR [ 117635]
  MRR-like [ 117638]
  PA4535-like [ 142449]
  XisH-like [ 159601]
  YaeQ-like [ 159605] (2)


Superfamily statistics
Genomes (3,188) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 19,765 91,410 63
Proteins 19,687 91,077 63


Functional annotation
General category Information
Detailed category DNA replication/repair

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)single-organism cellular process10.1182Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.19240.0000000001309Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.10560Least InformativeInherited
Biological Process (BP)response to stimulus0.94520.0004875Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.10840Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.30110.00000000000007357Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.16850Least InformativeInherited
Biological Process (BP)cellular response to stress0.0028870Moderately InformativeInherited
Biological Process (BP)DNA metabolic process0.0000024920InformativeDirect
Biological Process (BP)response to DNA damage stimulus0.000016140InformativeDirect
Molecular Function (MF)hydrolase activity0.55580.00000000001096Least InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds0.034320Moderately InformativeInherited
Molecular Function (MF)nuclease activity0.000020340InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.890.3188Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.20370.003963Least InformativeInherited
Cellular Component (CC)nuclear part0.00091820.000000002644Moderately InformativeDirect

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) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.00000000000007357 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0000000001309 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0.0004875 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.1182 Least Informative Inherited
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.000000003743 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.00000004127 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.1937 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.6301 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.8107 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.2606 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.1834 Moderately Informative Inherited
Biological Process (BP) reproduction 0.002958 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) cell cycle process 0.00009902 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.00000001867 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0 Informative Direct
Biological Process (BP) cellular process involved in reproduction 0.00000008517 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.0001465 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0 Informative Direct
Biological Process (BP) regulation of organelle organization 0.002991 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.04444 Informative Inherited
Biological Process (BP) response to light stimulus 0.2014 Informative Inherited
Biological Process (BP) DNA catabolic process 0 Highly Informative Direct
Biological Process (BP) DNA recombination 0.000000001006 Highly Informative Direct
Biological Process (BP) chromosome segregation 0.000004563 Highly Informative Direct
Biological Process (BP) meiosis 0.0000005716 Highly Informative Direct
Biological Process (BP) response to UV 0.0000000006116 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.0000006293 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.00000000001096 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.03588 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0 Informative Direct
Molecular Function (MF) DNA binding 0.00118 Informative Inherited
Molecular Function (MF) structure-specific DNA binding 0.000001066 Highly Informative Direct
Cellular Component (CC) protein complex 0.000001365 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.003963 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.3188 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.001202 Least Informative Inherited
Cellular Component (CC) nuclear part 0.000000002644 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00011 Moderately Informative Direct
Cellular Component (CC) chromosome 0.0042 Informative Inherited
Cellular Component (CC) nuclear chromosome part 0.0301 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)Acting on acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds1Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0Moderately InformativeDirect
Enzyme Commission (EC)Endodeoxyribonucleases producing 5'-phosphomonoest0Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)immune system disease0.00653Least InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.000299Moderately InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of head and neck0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the skull0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of brain morphology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skull size0InformativeDirect
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0InformativeDirect
Phenotypic Abnormality (PA)Abnormal eye physiology0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the cerebrum1InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)tumorigenesis0Moderately InformativeDirect
Mammalian Phenotype (MP)premature death0InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect

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)UV resistance0Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)chemical sensitive0Highly InformativeDirect

Document: FP 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)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately 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)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)DNA helicase0InformativeDirect
Enzyme Commission (EC)Exodeoxyribonucleases producing 5'-phosphomonoesters0Highly InformativeDirect
Enzyme Commission (EC)Endodeoxyribonucleases producing 5'-phosphomonoesters0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processHost-virus interaction0.2139Moderately InformativeInherited
Biological processDNA recombination0InformativeDirect
Biological processMeiosis0.0000000000008267InformativeDirect
Biological processEukaryotic host gene expression shutoff by virus1InformativeInherited
Biological processAntiviral defense0Highly InformativeDirect
Biological processDecay of host mRNAs by virus0.000000000001887Highly InformativeDirect
Cellular componentHost nucleus0.0000000000005919InformativeDirect
Cellular componentHost cytoplasm0.0007668InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionNucleotide-binding4.62e-16Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationExonuclease0InformativeDirect
Post-translational modificationHelicase0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011335 SSF52980 Protein matches
Abstract

This entry represents the core structure found in most type II restriction endonucleases, consisting of a 3-layer alpha/beta/alpha topology with mixed beta-sheets. This core structure can be found in the restriction endonucleases EcoRI, EcoRV, BamHI, BglI, BglII, BstyI, PvuII, MunI, NseI, NgoIV, BsobI, HincII, MspI, FokI (C-terminal), EcoO109IR, as well as in lamba exonuclease, DNA mismatch repair protein MutH, VSR (very short repair) endonucleases, TnsA endonucleases (N-terminal), endonucleases I (Holliday junction resolvase), Hjc-like enzymes, XPF/Rad1/Mus81 nucleases, RecB and RecC exodeoxyribonuclease V (C-terminal), and RecU-like enzymes.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · 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 41 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 Restriction endonuclease-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 41 hidden Markov models representing the Restriction endonuclease-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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]