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 (1,172) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 2,186 6,340 26
Proteins 1,839 5,115 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) heterocycle metabolic process 1.507e-07 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 1.904e-07 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.1676 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.001075 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.001056 Least Informative Inherited
Biological Process (BP) gene expression 0.002241 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.02685 Moderately Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 1.07e-05 Informative Direct
Biological Process (BP) RNA processing 0.02012 Informative Inherited
Biological Process (BP) DNA metabolic process 0.009064 Informative Inherited
Biological Process (BP) RNA splicing 1.211e-10 Highly Informative Direct
Biological Process (BP) DNA recombination 0.0003957 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.0001058 Least Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 1.598e-09 Moderately Informative Direct
Molecular Function (MF) nuclease activity 7.922e-16 Informative Direct
Cellular Component (CC) cytoplasmic part 0.001436 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01132 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 groups2.963e-05Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.01288Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides2.766e-09Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases4.506e-07Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.001076Moderately InformativeInherited
Enzyme Commission (EC)DNA-directed DNA polymerase1.488e-13InformativeDirect
Enzyme Commission (EC)DNA helicase6.035e-11InformativeDirect
Enzyme Commission (EC)DNA topoisomerase (ATP-hydrolyzing)0Highly InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; catalyzing transmembrane movement of substances0.4388Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation4.942e-08Moderately InformativeDirect
Biological processDNA damage0.6488Moderately InformativeInherited
Biological processDNA replication1.055e-12InformativeDirect
Biological processmRNA splicing1.256e-10InformativeDirect
Biological processIntron homing0Highly InformativeDirect
Biological processSOS response0.000398Highly InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentPrimosome2.484e-09Highly InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationHydrolase4.438e-16Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.001038Moderately InformativeInherited
Post-translational modificationIsomerase0.3959Moderately InformativeInherited
Post-translational modificationDNA-directed DNA polymerase1.384e-13InformativeDirect
Post-translational modificationEndonuclease2.904e-13InformativeDirect
Post-translational modificationTopoisomerase2.871e-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 ]