SUPERFAMILY 1.75 HMM library and genome assignments server


Homing endonucleases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Homing endonuclease-like [ 55603] (2)
Superfamily:   Homing endonucleases [ 55608] (2)
Families:   Group I mobile intron endonuclease [ 55609] (5)
  Intein endonuclease [ 55614] (2)


Superfamily statistics
Genomes (1,188) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,217 13,158 26
Proteins 1,860 11,408 18


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 1.211e-08 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0002751 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 9.358e-09 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0002656 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0879 Least Informative Inherited
Biological Process (BP) gene expression 0.002149 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.02124 Moderately Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 4.202e-06 Informative Direct
Biological Process (BP) RNA processing 0.009478 Informative Inherited
Biological Process (BP) DNA metabolic process 0.005071 Informative Inherited
Biological Process (BP) DNA recombination 0.0001074 Highly Informative Direct
Biological Process (BP) RNA splicing 6.003e-12 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.0002853 Least Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 2.735e-10 Moderately Informative Direct
Molecular Function (MF) nuclease activity 0 Informative Direct
Cellular Component (CC) cytoplasmic part 0.00041 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.03918 Least 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 anhydrides3.686e-09Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases2.792e-07Least InformativeDirect
Enzyme Commission (EC)Isomerases0.001094Least InformativeInherited
Enzyme Commission (EC)DNA-directed DNA polymerase2.981e-13Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0.01072Moderately InformativeInherited
Enzyme Commission (EC)Sole sub-subclass for isomerases that do not belon1InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides; catalyzing transmembran0.4538InformativeInherited
Enzyme Commission (EC)H(+)-transporting two-sector ATPase4.991e-06Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups8.526e-05Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.004349Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases0.981Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides8.514e-11Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases4.283e-07Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.00177Moderately InformativeInherited
Enzyme Commission (EC)DNA-directed DNA polymerase1.572e-13InformativeDirect
Enzyme Commission (EC)DNA helicase1.967e-13InformativeDirect
Enzyme Commission (EC)Acting on CH or CH(2) groups0.0001682InformativeDirect
Enzyme Commission (EC)DNA topoisomerase (ATP-hydrolyzing)2.426e-16Highly InformativeDirect
Enzyme Commission (EC)With a disulfide as acceptor2.342e-07Highly InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; catalyzing transmembrane movement of substances0.6014Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation7.68e-08Moderately InformativeDirect
Biological processDNA damage0.3729Moderately InformativeInherited
Biological processDNA replication2.264e-13InformativeDirect
Biological processmRNA splicing1.509e-10InformativeDirect
Biological processIntron homing0Highly InformativeDirect
Biological processSOS response0.0003987Highly InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentPrimosome2.489e-09Highly InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationHydrolase6.651e-16Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.001055Moderately InformativeInherited
Post-translational modificationIsomerase0.4021Moderately InformativeInherited
Post-translational modificationDNA-directed DNA polymerase1.514e-13InformativeDirect
Post-translational modificationEndonuclease3.421e-13InformativeDirect
Post-translational modificationTopoisomerase3.227e-11Highly InformativeDirect
Post-translational modificationAutocatalytic cleavage0InformativeDirect
Post-translational modificationProtein splicing0Highly InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · 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 13 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 Homing endonucleases 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 13 hidden Markov models representing the Homing endonucleases 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 · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]