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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 (3,197) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 19,809 118,502 63
Proteins 19,730 117,903 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)response to stimulus10.001233Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.39490Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.41470Least InformativeInherited
Biological Process (BP)macromolecule metabolic process0.5480.0000000003007Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.29260Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.29530Least InformativeInherited
Biological Process (BP)primary metabolic process10.00001186Least InformativeInherited
Biological Process (BP)cellular response to stress0.0067180Moderately InformativeInherited
Biological Process (BP)DNA metabolic process0.000051690InformativeDirect
Biological Process (BP)cellular response to DNA damage stimulus0.00011140InformativeDirect
Molecular Function (MF)hydrolase activity0.28390.0000000000006406Least InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds0.0034360Moderately InformativeInherited
Molecular Function (MF)nuclease activity0.00000013960InformativeDirect

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) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0000000003007 Least Informative Direct
Biological Process (BP) primary metabolic process 0.00001186 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.001233 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.6324 Least Informative Inherited
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0.00727 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.1556 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.6149 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.5071 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.795 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.7963 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.2147 Moderately Informative Inherited
Biological Process (BP) reproduction 0.001871 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) cell cycle process 0.000001209 Informative Direct
Biological Process (BP) response to radiation 0.00001307 Informative Direct
Biological Process (BP) single organism reproductive process 0.00008997 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.0007227 Informative Direct
Biological Process (BP) regulation of organelle organization 0.001315 Informative Inherited
Biological Process (BP) nuclear division 0.0000000000153 Highly Informative Direct
Biological Process (BP) meiotic cell cycle 0.0000000001799 Highly Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.0000000005491 Highly Informative Direct
Biological Process (BP) DNA recombination 0.000000001315 Highly Informative Direct
Biological Process (BP) negative regulation of homeostatic process 0.000000004744 Highly Informative Direct
Biological Process (BP) response to UV 0.00000000692 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.00000006212 Highly Informative Direct
Biological Process (BP) nuclear chromosome segregation 0.00003077 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.00008348 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.0000000000006406 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 0.1213 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0 Informative Direct
Molecular Function (MF) DNA binding 0.005376 Informative Inherited
Molecular Function (MF) deoxyribonuclease activity 0 Highly Informative Direct
Molecular Function (MF) single-stranded DNA binding 0.0000000002361 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.3343 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.1357 Least Informative Inherited
Cellular Component (CC) protein complex 0.01243 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.7113 Least Informative Inherited
Cellular Component (CC) nuclear part 0.000003977 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00221 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.0001567 Informative Direct
Cellular Component (CC) nuclear chromosome part 0.02123 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processHost-virus interaction0.00000004659Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processDNA repair0InformativeDirect
Biological processMeiosis0.000000000006298InformativeDirect
Biological processEukaryotic host gene expression shutoff by virus1InformativeInherited
Biological processDecay of host mRNAs by virus0.000000000001761Highly InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionNucleotide-binding0.00000000001216Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationHelicase0InformativeDirect
Post-translational modificationExonuclease0InformativeDirect

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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]