SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.

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 (1,189) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 2,225 17,476 26
Proteins 1,864 14,190 18

Functional annotation
General category Information
Detailed category DNA replication/repair

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 0.000004612 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.000005476 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.000008982 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00009447 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0001169 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0005493 Least Informative Direct
Biological Process (BP) RNA metabolic process 0.4412 Moderately Informative Inherited
Biological Process (BP) gene expression 0.001449 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.03319 Informative Inherited
Biological Process (BP) RNA splicing 0.0000000000002035 Highly Informative Direct
Biological Process (BP) DNA recombination 0.00000009117 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.0002141 Least Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.0006022 Moderately Informative Direct
Molecular Function (MF) nuclease activity 0.000000000002929 Informative Direct
Cellular Component (CC) cytoplasmic part 0.001881 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.03021 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 anhydrides0.000000003686Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0.0000002792Least InformativeDirect
Enzyme Commission (EC)Isomerases0.001094Least InformativeInherited
Enzyme Commission (EC)DNA-directed DNA polymerase0.0000000000002981Moderately 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 ATPase0.000004991Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0.0000001829Moderately InformativeDirect
Biological processDNA damage0.3323Moderately InformativeInherited
Biological processDNA replication0.0000000000002258InformativeDirect
Biological processmRNA processing0.0000003775InformativeDirect
Biological processIntron homing0Highly InformativeDirect
Biological processSOS response0.0007301Highly InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentPrimosome0.000000002322Highly InformativeDirect
Post-translational modificationHydrolase0.000000000001958Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.0009266Moderately InformativeDirect
Post-translational modificationIsomerase0.5547Moderately InformativeInherited
Post-translational modificationEndonuclease0.0000000000002999InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0.0000000000002015Highly InformativeDirect
Post-translational modificationTopoisomerase0.00000000003403Highly 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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]