SUPERFAMILY 1.75 HMM library and genome assignments server


His-Me finger endonucleases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   His-Me finger endonucleases [ 54059]
Superfamily:   His-Me finger endonucleases [ 54060] (6)
Families:   Endonuclease I [ 102726]
  HNH-motif [ 54061] (2)
  DNA/RNA non-specific endonuclease [ 54066] (2)
  Intron-encoded homing endonucleases [ 54069] (2)
  Recombination endonuclease VII, N-terminal domain [ 68915]
  Caspase-activated DNase, CAD (DffB, DFF40) [ 110778]


Superfamily statistics
Genomes (1,568) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,008 18,386 24
Proteins 4,904 18,001 24


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 2.743e-07 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 5.969e-09 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 1.868e-07 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 7.01e-07 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.2114 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.5759 Least Informative Inherited
Biological Process (BP) cellular catabolic process 9.023e-11 Moderately Informative Direct
Biological Process (BP) organic cyclic compound catabolic process 3.212e-07 Moderately Informative Direct
Biological Process (BP) DNA metabolic process 3.503e-05 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 6.694e-07 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 1.063e-06 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 5.618e-15 Informative Direct
Biological Process (BP) apoptotic process 0.4042 Informative Inherited
Biological Process (BP) DNA catabolic process 1.716e-12 Highly Informative Direct
Biological Process (BP) cellular component disassembly 4.041e-10 Highly Informative Direct
Biological Process (BP) execution phase of apoptosis 2.462e-14 Highly Informative Direct
Molecular Function (MF) hydrolase activity 3.603e-14 Least Informative Direct
Molecular Function (MF) binding 0.454 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 8.399e-06 Moderately Informative Direct
Molecular Function (MF) cation binding 4.788e-05 Moderately Informative Direct
Molecular Function (MF) nuclease activity 1.679e-12 Informative Direct
Molecular Function (MF) transition metal ion binding 7.094e-07 Informative Direct
Molecular Function (MF) phosphoric ester hydrolase activity 1 Informative Inherited
Molecular Function (MF) calcium ion binding 1.602e-09 Highly Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 2.332e-15 Highly Informative Direct
Molecular Function (MF) carboxylic ester hydrolase activity 0.2 Highly Informative Inherited
Molecular Function (MF) lipase activity 0.1521 Highly Informative Inherited
Cellular Component (CC) membrane 0.06843 Least Informative Inherited
Cellular Component (CC) extracellular region part 0.0003174 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.1716 Moderately Informative Inherited
Cellular Component (CC) intrinsic to membrane 0.001883 Moderately Informative Inherited
Cellular Component (CC) intrinsic to plasma membrane 5.013e-05 Informative Direct
Cellular Component (CC) integral to membrane 0.001193 Informative Inherited
Cellular Component (CC) integral to plasma membrane 2.853e-05 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.0196Least InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases6.077e-14Moderately InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides4.777e-13Moderately InformativeDirect
Enzyme Commission (EC)Nucleotide diphosphatase0Highly InformativeDirect
Enzyme Commission (EC)Phosphodiesterase I8.244e-14Highly InformativeDirect

Document: EC annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)fertile0Moderately InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.003953Moderately InformativeInherited
Enzyme Commission (EC)In phosphorous-containing anhydrides2.422e-16InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases4.814e-16InformativeDirect
Enzyme Commission (EC)Endodeoxyribonucleases producing 5'-phosphomonoesters0.001582Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis1.247e-06Moderately InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentMitochondrion8.783e-06Moderately InformativeDirect
DiseaseObesity8.789e-11InformativeDirect
DomainSignal0.0003167Least InformativeDirect
DomainTransmembrane1Least InformativeInherited
DomainTransit peptide0.0003137Moderately InformativeDirect
DomainSignal-anchor6.573e-10InformativeDirect
Molecular functionMetal-binding2.538e-09Least InformativeDirect
Molecular functionZinc2.164e-07Least InformativeDirect
Molecular functionCalcium1.198e-06Moderately InformativeDirect
Molecular functionManganese2.129e-05Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationAntimicrobial2.104e-09InformativeDirect
Post-translational modificationAntibiotic1.296e-11Highly InformativeDirect
Post-translational modificationGlycoprotein9.988e-07Least InformativeDirect
Post-translational modificationDisulfide bond1.899e-06Least InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · 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 9 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 His-Me finger 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 9 hidden Markov models representing the His-Me finger 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) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]