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 (883)	Uniprot 2013_05	PDB chains (SCOP 1.75)
Domains	1,754	6,340	26
Proteins	1,450	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	4.576e-06	Least Informative	Direct
Biological Process (BP)	cellular aromatic compound metabolic process	6.028e-06	Least Informative	Direct
Biological Process (BP)	organic cyclic compound metabolic process	1.293e-05	Least Informative	Direct
Biological Process (BP)	nitrogen compound metabolic process	3.856e-05	Least Informative	Direct
Biological Process (BP)	cellular macromolecule metabolic process	0.0003281	Least Informative	Direct
Biological Process (BP)	RNA metabolic process	0.02516	Moderately Informative	Inherited
Biological Process (BP)	gene expression	0.02694	Moderately Informative	Inherited
Biological Process (BP)	DNA metabolic process	0.00253	Informative	Inherited
Biological Process (BP)	DNA recombination	1.316e-09	Highly Informative	Direct
Molecular Function (MF)	hydrolase activity	0.0001339	Least Informative	Direct
Molecular Function (MF)	hydrolase activity, acting on ester bonds	1.789e-09	Moderately Informative	Direct
Molecular Function (MF)	nuclease activity	7.973e-16	Informative	Direct
Cellular Component (CC)	cytoplasmic part	0.0001488	Least Informative	Direct
Cellular Component (CC)	intracellular membrane-bounded organelle	0.0005682	Least Informative	Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Acting on acid anhydrides	3.686e-09	Least Informative	Direct
Enzyme Commission (EC)	Nucleotidyltransferases	2.792e-07	Least Informative	Direct
Enzyme Commission (EC)	Isomerases	0.001094	Least Informative	Inherited
Enzyme Commission (EC)	DNA-directed DNA polymerase	2.981e-13	Moderately Informative	Direct
Enzyme Commission (EC)	Acting on acid anhydrides; involved in cellular an	0.01072	Moderately Informative	Inherited
Enzyme Commission (EC)	Sole sub-subclass for isomerases that do not belon	1	Informative	Inherited
Enzyme Commission (EC)	Acting on acid anhydrides; catalyzing transmembran	0.4538	Informative	Inherited
Enzyme Commission (EC)	H(+)-transporting two-sector ATPase	4.991e-06	Highly Informative	Direct

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Transferring phosphorous-containing groups	2.976e-05	Least Informative	Direct
Enzyme Commission (EC)	Hydrolases	0.01354	Least Informative	Inherited
Enzyme Commission (EC)	Acting on acid anhydrides	3.129e-09	Moderately Informative	Direct
Enzyme Commission (EC)	Nucleotidyltransferases	3.196e-07	Moderately Informative	Direct
Enzyme Commission (EC)	Isomerases	0.001191	Moderately Informative	Inherited
Enzyme Commission (EC)	DNA-directed DNA polymerase	2.36e-13	Informative	Direct
Enzyme Commission (EC)	DNA helicase	6.332e-11	Informative	Direct
Enzyme Commission (EC)	DNA topoisomerase (ATP-hydrolyzing)	0	Highly Informative	Direct
Enzyme Commission (EC)	Acting on acid anhydrides; catalyzing transmembrane movement of substances	0.4436	Highly Informative	Inherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)

Highlighted in gray are those with FDR_all>0.001

	KW term	FDR (all)	IC level	SDKW level	Annotation (direct or inherited)
Biological process	Transcription	0	0.8219	--	DIRECT
Biological process	mRNA processing	8.685e-07	1.301	--	DIRECT
Biological process	DNA repair	0.9653	1.225	--	INHERITED FROM: SOS response
Biological process	Transcription regulation	5.404e-08	0.8763	Moderately Informative	DIRECT
Biological process	DNA damage	0.3977	1.202	Moderately Informative	INHERITED FROM: SOS response
Biological process	DNA replication	1.074e-14	1.46	Informative	DIRECT
Biological process	mRNA splicing	1.172e-10	1.575	Informative	DIRECT
Biological process	SOS response	0.0004116	2.015	Highly Informative	DIRECT
Cellular component	Mitochondrion	0	0.9365	Moderately Informative	DIRECT
Cellular component	Primosome	6.402e-10	2.095	Highly Informative	DIRECT
Molecular function	ATP-binding	0.9111	0.7016	--	INHERITED FROM: Helicase
Molecular function	Nucleotide-binding	1	0.6016	Least Informative	INHERITED FROM: Helicase
Molecular function	DNA-binding	0	0.7568	Moderately Informative	DIRECT
Molecular function	Helicase	3.822e-05	1.342	Informative	DIRECT
Post-translational modification	Hydrolase	4.42e-16	0.5298	Least Informative	DIRECT
Post-translational modification	Transferase	1	0.5454	Least Informative	INHERITED FROM: Nucleotidyltransferase \|\| DNA-directed DNA polymerase
Post-translational modification	Nuclease	0	1.188	Moderately Informative	DIRECT
Post-translational modification	Nucleotidyltransferase	0.0008463	1.159	Moderately Informative	DIRECT
Post-translational modification	Isomerase	0.4004	1.217	Moderately Informative	INHERITED FROM: Topoisomerase
Post-translational modification	Endonuclease	1.16e-13	1.338	Informative	DIRECT
Post-translational modification	DNA-directed DNA polymerase	1.708e-13	1.72	Informative	DIRECT
Post-translational modification	Intron homing	0	2.217	Highly Informative	DIRECT
Post-translational modification	Topoisomerase	3.025e-11	1.949	Highly Informative	DIRECT
Post-translational modification	Autocatalytic cleavage	0	1.464	Informative	DIRECT
Post-translational modification	Protein splicing	0	1.799	Highly Informative	DIRECT

	KW term	FDR (all)	SDKW level	Annotation (direct or inherited)
Biological process	Transcription regulation	5.404e-08	Moderately Informative	Direct
Biological process	DNA damage	0.3977	Moderately Informative	Inherited
Biological process	DNA replication	1.074e-14	Informative	Direct
Biological process	mRNA splicing	1.172e-10	Informative	Direct
Biological process	SOS response	0.0004116	Highly Informative	Direct
Cellular component	Mitochondrion	0	Moderately Informative	Direct
Cellular component	Primosome	6.402e-10	Highly Informative	Direct
Molecular function	Nucleotide-binding	1	Least Informative	Inherited
Molecular function	DNA-binding	0	Moderately Informative	Direct
Molecular function	Helicase	3.822e-05	Informative	Direct
Post-translational modification	Hydrolase	4.42e-16	Least Informative	Direct
Post-translational modification	Transferase	1	Least Informative	Inherited
Post-translational modification	Nuclease	0	Moderately Informative	Direct
Post-translational modification	Nucleotidyltransferase	0.0008463	Moderately Informative	Direct
Post-translational modification	Isomerase	0.4004	Moderately Informative	Inherited
Post-translational modification	Endonuclease	1.16e-13	Informative	Direct
Post-translational modification	DNA-directed DNA polymerase	1.708e-13	Informative	Direct
Post-translational modification	Intron homing	0	Highly Informative	Direct
Post-translational modification	Topoisomerase	3.025e-11	Highly Informative	Direct
Post-translational modification	Autocatalytic cleavage	0	Informative	Direct
Post-translational modification	Protein splicing	0	Highly Informative	Direct

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 ]

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Homing endonucleases superfamily