SUPERFAMILY 1.75 HMM library and genome assignments server


DNA-glycosylase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   DNA-glycosylase [ 48149]
Superfamily:   DNA-glycosylase [ 48150] (6)
Families:   Endonuclease III [ 48151]
  Mismatch glycosylase [ 48154] (3)
  3-Methyladenine DNA glycosylase I (Tag) [ 74756]
  3-Methyladenine DNA glycosylase III (MagIII) [ 101349]
  DNA repair glycosylase, 2 C-terminal domains [ 48157] (2)
  AgoG-like [ 116976] (2)


Superfamily statistics
Genomes (3,098) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 12,594 28,720 36
Proteins 12,563 28,687 36


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular aromatic compound metabolic process6.463e-080Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process1.106e-060Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process3.248e-076.044e-14Least InformativeDirect
Biological Process (BP)single-organism cellular process0.00023950.0005425Least InformativeDirect
Biological Process (BP)heterocycle metabolic process5.876e-080Least InformativeDirect
Biological Process (BP)response to stimulus5.759e-058.12e-13Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process2.02e-070Least InformativeDirect
Biological Process (BP)macromolecule catabolic process0.00034799.447e-12Moderately InformativeDirect
Biological Process (BP)cellular response to stress1.603e-120Moderately InformativeDirect
Biological Process (BP)cellular catabolic process0.0078881.066e-06Moderately InformativeInherited
Biological Process (BP)organic cyclic compound catabolic process0.0066214.659e-08Moderately InformativeInherited
Biological Process (BP)DNA metabolic process00InformativeDirect
Biological Process (BP)response to DNA damage stimulus00InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process7.635e-052.638e-13InformativeDirect
Biological Process (BP)nucleobase-containing compound catabolic process0.017053.209e-06InformativeInherited
Biological Process (BP)DNA modification3.558e-050Highly InformativeDirect
Biological Process (BP)DNA catabolic process6.464e-060Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.0084257.922e-16Least InformativeInherited
Molecular Function (MF)lyase activity0.00015730Moderately InformativeDirect
Molecular Function (MF)hydrolase activity, acting on glycosyl bonds6.69e-100InformativeDirect
Molecular Function (MF)hydrolase activity, hydrolyzing N-glycosyl compounds1.239e-140Highly InformativeDirect

Document: GO annotation of SCOP domains

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 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 6.044e-14 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0005425 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) response to stimulus 8.12e-13 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.1668 Least Informative Inherited
Biological Process (BP) macromolecule catabolic process 9.447e-12 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 1.066e-06 Moderately Informative Direct
Biological Process (BP) organic cyclic compound catabolic process 4.659e-08 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.5806 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.05888 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.3395 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.8608 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.04989 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) nucleobase-containing compound catabolic process 3.209e-06 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 2.638e-13 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 3.173e-08 Informative Direct
Biological Process (BP) organophosphate catabolic process 0.1288 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.1677 Informative Inherited
Biological Process (BP) DNA modification 0 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0 Highly Informative Direct
Biological Process (BP) deoxyribonucleotide metabolic process 6.366e-14 Highly Informative Direct
Biological Process (BP) deoxyribose phosphate metabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 3.856e-13 Highly Informative Direct
Molecular Function (MF) hydrolase activity 7.922e-16 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.03925 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on glycosyl bonds 0 Informative Direct
Molecular Function (MF) DNA binding 0.003105 Informative Inherited
Molecular Function (MF) hydrolase activity, hydrolyzing N-glycosyl compounds 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.001164 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 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)Lyases0Least InformativeDirect
Enzyme Commission (EC)Other carbon-oxygen lyases0InformativeDirect
Enzyme Commission (EC)Hydrolyzing N-glycosyl compounds6.815e-12InformativeDirect
Enzyme Commission (EC)DNA-(apurinic or apyrimidinic site) lyase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0Least InformativeDirect
Mammalian Phenotype (MP)tumorigenesis0.002397Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.007045InformativeInherited
Mammalian Phenotype (MP)increased adenoma incidence8.555e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal DNA repair4.575e-05Highly InformativeDirect
Mammalian Phenotype (MP)decreased physiological sensitivity to xenobiotic6.614e-05Highly InformativeDirect

Document: MP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)head0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Glycosylases1.922e-06Moderately InformativeDirect
Enzyme Commission (EC)Other carbon-oxygen lyases0Highly InformativeDirect
Enzyme Commission (EC)Hydrolyzing N-glycosyl compounds7.126e-12Highly InformativeDirect

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 excision1.315e-11Highly InformativeDirect
Cellular componentNucleus3.965e-06Least InformativeDirect
Molecular functionDNA-binding8.79e-11Least InformativeDirect
Molecular functionMetal-binding2.42e-10Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationGlycosidase0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011257 SSF48150 Protein matches
Abstract

DNA glycosylases act to repair oxidative damage in DNA. These proteins are redundant as there are several different types of DNA glycosylases that are ale to compensate for one another. Examples include the endonuclease III subfamily, the mismatch glycosylases subfamily, the 3-methyladenine DNA glycosylases I subfamily, and the DNA repair glycosylases subfamily [PubMed14637253].


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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 12 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 DNA-glycosylase 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 12 hidden Markov models representing the DNA-glycosylase 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]