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 (1,569) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,027 18,386 24
Proteins 4,914 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 0.0000002744 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.000000006838 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0000001883 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0000007348 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.4697 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.2331 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.5325 Least Informative Inherited
Biological Process (BP) cellular catabolic process 0.00000000008046 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0000000005625 Moderately Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.0000005706 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.000001191 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.000000000000003707 Informative Direct
Biological Process (BP) apoptotic process 0.3464 Informative Inherited
Biological Process (BP) DNA catabolic process 0.000000000001439 Highly Informative Direct
Biological Process (BP) cellular component disassembly 0.0000000003705 Highly Informative Direct
Biological Process (BP) execution phase of apoptosis 0.00000000000003082 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.00000000000002949 Least Informative Direct
Molecular Function (MF) binding 0.3425 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0 Moderately Informative Direct
Molecular Function (MF) cation binding 0.0000549 Moderately Informative Direct
Molecular Function (MF) nuclease activity 0.000000000003027 Informative Direct
Molecular Function (MF) zinc ion binding 0.00000001111 Informative Direct
Molecular Function (MF) calcium ion binding 0.000000001624 Highly Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 0.000000000000003138 Highly Informative Direct
Molecular Function (MF) carboxylic ester hydrolase activity 0.1913 Highly Informative Inherited
Molecular Function (MF) lipase activity 0.1359 Highly Informative Inherited
Cellular Component (CC) membrane 0.1236 Least Informative Inherited
Cellular Component (CC) extracellular region part 0.0003017 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 0.004903 Moderately Informative Inherited
Cellular Component (CC) intrinsic component of membrane 0.001802 Moderately Informative Inherited
Cellular Component (CC) intrinsic component of plasma membrane 0.00004424 Informative Direct
Cellular Component (CC) integral component of membrane 0.001151 Informative Inherited
Cellular Component (CC) integral component of plasma membrane 0.00002528 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 hydrolases0.00000000000006077Moderately InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides0.0000000000004777Moderately InformativeDirect
Enzyme Commission (EC)Nucleotide diphosphatase0Highly InformativeDirect
Enzyme Commission (EC)Phosphodiesterase I0.00000000000008244Highly 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 anhydrides0.003793Moderately InformativeInherited
Enzyme Commission (EC)In phosphorous-containing anhydrides2.432e-16InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases4.839e-16InformativeDirect
Enzyme Commission (EC)Endodeoxyribonucleases producing 5'-phosphomonoesters0.001574Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis0.000001247Moderately InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentMitochondrion0.000008826Moderately InformativeDirect
DiseaseObesity0.000000000087InformativeDirect
DomainSignal0.0003146Least InformativeDirect
DomainTransmembrane1Least InformativeInherited
DomainTransit peptide0.000317Moderately InformativeDirect
DomainSignal-anchor0.0000000006637InformativeDirect
Molecular functionMetal-binding0.000000003362Least InformativeDirect
Molecular functionZinc0.0000002395Least InformativeDirect
Molecular functionCalcium0.000001315Moderately InformativeDirect
Molecular functionManganese0.00002222Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationAntimicrobial0.000000002091InformativeDirect
Post-translational modificationAntibiotic0.00000000001288Highly InformativeDirect
Post-translational modificationGlycoprotein0.000001037Least InformativeDirect
Post-translational modificationDisulfide bond0.000001921Least 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 ]