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 (3,139) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 13,003 64,497 36
Proteins 12,964 64,452 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 process0.000000013090Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.00000028550Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.000000056760.000000000000007248Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.000095860.000000000002644Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.000000012190Least InformativeDirect
Biological Process (BP)response to stimulus0.000020410.00000000001585Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.000000045430Least InformativeDirect
Biological Process (BP)single-organism cellular process0.0014440.02773Least InformativeInherited
Biological Process (BP)cellular response to stress0.000000000000091460Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process0.030010.00005451Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.013680.000007345Moderately InformativeInherited
Biological Process (BP)DNA repair00InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process0.00015630.000000000005887InformativeDirect
Biological Process (BP)nucleobase-containing compound catabolic process0.027380.00001616InformativeInherited
Biological Process (BP)DNA modification0.000058590Highly InformativeDirect
Biological Process (BP)DNA catabolic process0.0000089820Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.0000093650Least InformativeDirect
Molecular Function (MF)lyase activity0.00039190.000000000000001593Moderately InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds0.2590.004407Moderately InformativeInherited
Molecular Function (MF)nuclease activity0.00000028390InformativeDirect
Molecular Function (MF)hydrolase activity, acting on glycosyl bonds0.00000013950InformativeDirect
Molecular Function (MF)hydrolase activity, hydrolyzing N-glycosyl compounds00Highly 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 0.000000000000007248 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.000000000002644 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0.00000000001585 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.02773 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.4165 Least Informative Inherited
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.000007345 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.00005451 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.6796 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.1566 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.4146 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.9259 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.03011 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.2667 Moderately Informative Inherited
Biological Process (BP) DNA repair 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.00001616 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.000000000005887 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.0000002033 Informative Direct
Biological Process (BP) organophosphate catabolic process 0.09911 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.129 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 0.0000000000000615 Highly Informative Direct
Biological Process (BP) deoxyribose phosphate metabolic process 0.000000000000001913 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.00000000002745 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) lyase activity 0.000000000000001593 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.004407 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0 Informative Direct
Molecular Function (MF) hydrolase activity, acting on glycosyl bonds 0 Informative Direct
Molecular Function (MF) hydrolase activity, hydrolyzing N-glycosyl compounds 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00001682 Least Informative Direct
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 compounds0.000000000006815InformativeDirect
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)tumorigenesis0.002514Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.008813Moderately InformativeInherited
Mammalian Phenotype (MP)increased adenoma incidence0.000008617Highly InformativeDirect
Mammalian Phenotype (MP)abnormal DNA repair0.00005013Highly InformativeDirect
Mammalian Phenotype (MP)decreased physiological sensitivity to xenobiotic0.00006761Highly 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)Glycosylases0.00000502Moderately InformativeDirect
Enzyme Commission (EC)Other carbon-oxygen lyases0Highly InformativeDirect
Enzyme Commission (EC)Hydrolyzing N-glycosyl compounds0.00000000001889Highly 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 excision0.00000000001928Highly InformativeDirect
Cellular componentNucleus0.00000000005628Least InformativeDirect
Cellular componentMitochondrion0.0001761Moderately InformativeDirect
DomainTransit peptide0.00002297Moderately InformativeDirect
Molecular functionMetal-binding0.00000000001725Least InformativeDirect
Molecular functionDNA-binding0.0000000003648Least 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 ]