SUPERFAMILY 1.75 HMM library and genome assignments server


C-terminal domain of Ku80 superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   alpha-alpha superhelix [ 48370] (24)
Superfamily:   C-terminal domain of Ku80 [ 101420]
Families:   C-terminal domain of Ku80 [ 101421]


Superfamily statistics
Genomes (342) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 432 0 2
Proteins 408 0 2


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 2.913e-11 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 2.803e-10 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 2.426e-09 Least Informative Direct
Biological Process (BP) single-organism cellular process 2.258e-08 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 2.312e-11 Least Informative Direct
Biological Process (BP) response to stimulus 1.397e-10 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 7.645e-11 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.001416 Least Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.0008107 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) homeostatic process 2.874e-07 Moderately Informative Direct
Biological Process (BP) organelle organization 0.0457 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) chromosome organization 5.153e-08 Informative Direct
Biological Process (BP) double-strand break repair 0 Highly Informative Direct
Biological Process (BP) response to ionizing radiation 0 Highly Informative Direct
Biological Process (BP) cellular response to radiation 5.97e-06 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.004686 Least Informative Inherited
Molecular Function (MF) binding 0.04916 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 6.735e-07 Moderately Informative Direct
Molecular Function (MF) DNA binding 3.558e-08 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 9.605e-07 Informative Direct
Molecular Function (MF) structure-specific DNA binding 5.41e-06 Highly Informative Direct
Cellular Component (CC) protein complex 0.0003817 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.007678 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.001575 Least Informative Inherited
Cellular Component (CC) nuclear part 0.0003182 Moderately 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 acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0Moderately InformativeDirect

Document: EC 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 anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)DNA helicase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Cellular componentTelomere8.415e-08Highly InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationHelicase0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR014893 SSF101420 Protein matches
Abstract

The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ. Ku has affinity for DNA ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This domain is found at the C terminal of Ku which binds to DNA-PKcs [PubMed14672664].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · 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 1 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 C-terminal domain of Ku80 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 1 hidden Markov models representing the C-terminal domain of Ku80 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]