SUPERFAMILY 1.75 HMM library and genome assignments server

DNA-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   DNA-binding domain [ 54170]
Superfamily:   DNA-binding domain [ 54171] (4)
Families:   DNA-binding domain from tn916 integrase [ 54172]
  lambda integrase N-terminal domain [ 75344]
  GCC-box binding domain [ 54175]
  Methyl-CpG-binding domain, MBD [ 54178] (2)


Superfamily statistics
Genomes (466) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 15,740 17,170 10
Proteins 13,530 15,580 10


Functional annotation
General category Regulation
Detailed category DNA-binding

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) response to stimulus 0.000000000000304 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.02074 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.1154 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.9215 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.02185 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 1 Least Informative Inherited
Biological Process (BP) developmental process 0.004676 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.02748 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.01832 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.1587 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.5546 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.2081 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.1761 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.371 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.1867 Least Informative Inherited
Biological Process (BP) response to endogenous stimulus 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.000000000001816 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.00000000006099 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.00000003354 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.0000001837 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.000001181 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.000001321 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.000001713 Moderately Informative Direct
Biological Process (BP) single-organism organelle organization 0.00002381 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.0003303 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.3129 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.14 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) organ development 0.4993 Moderately Informative Inherited
Biological Process (BP) reproductive process 0.008269 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.7104 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.001034 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.4891 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.6439 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.1215 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.5583 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.02249 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.0609 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.8565 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.01674 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.03915 Moderately Informative Inherited
Biological Process (BP) tissue development 0.7201 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) defense response 0.304 Moderately Informative Inherited
Biological Process (BP) immune system process 0.4356 Moderately Informative Inherited
Biological Process (BP) response to acid chemical 0.0000000000000883 Informative Direct
Biological Process (BP) chromosome organization 0.0000000000004488 Informative Direct
Biological Process (BP) intracellular signal transduction 0.000000000003727 Informative Direct
Biological Process (BP) cellular response to hormone stimulus 0.00000001161 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.00000005656 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.000003734 Informative Direct
Biological Process (BP) response to inorganic substance 0.0001424 Informative Direct
Biological Process (BP) reproductive structure development 0.0001461 Informative Direct
Biological Process (BP) immune effector process 0.0002832 Informative Direct
Biological Process (BP) cytoplasmic transport 0.2219 Informative Inherited
Biological Process (BP) single-organism intracellular transport 0.09794 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.04496 Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle 0.2515 Informative Inherited
Biological Process (BP) single-organism cellular localization 0.01344 Informative Inherited
Biological Process (BP) regulation of growth 0.02121 Informative Inherited
Biological Process (BP) protein localization to organelle 0.1203 Informative Inherited
Biological Process (BP) cell cycle process 0.08982 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.1739 Informative Inherited
Biological Process (BP) response to organonitrogen compound 0.04466 Informative Inherited
Biological Process (BP) single organism reproductive process 0.01131 Informative Inherited
Biological Process (BP) response to lipid 0.01209 Informative Inherited
Biological Process (BP) regulation of cell cycle process 0.03952 Informative Inherited
Biological Process (BP) protein transport 0.03537 Informative Inherited
Biological Process (BP) embryonic organ development 0.06174 Informative Inherited
Biological Process (BP) tube development 0.6796 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.7386 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.7405 Informative Inherited
Biological Process (BP) cardiovascular system development 0.942 Informative Inherited
Biological Process (BP) organ morphogenesis 0.7753 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) response to water deprivation 0 Highly Informative Direct
Biological Process (BP) hormone-mediated signaling pathway 0 Highly Informative Direct
Biological Process (BP) gene silencing 0.0000000000002434 Highly Informative Direct
Biological Process (BP) regulation of multicellular organism growth 0.000000000001496 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.0000000001791 Highly Informative Direct
Biological Process (BP) response to cold 0.0000000005508 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.000000002824 Highly Informative Direct
Biological Process (BP) post-embryonic development 0.00000000548 Highly Informative Direct
Biological Process (BP) protein deacylation 0.000000006317 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.00000002714 Highly Informative Direct
Biological Process (BP) DNA modification 0.000000241 Highly Informative Direct
Biological Process (BP) internal protein amino acid acetylation 0.000001449 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-templated 0.00000177 Highly Informative Direct
Biological Process (BP) response to fungus 0.00002669 Highly Informative Direct
Biological Process (BP) single-organism nuclear import 0.00004895 Highly Informative Direct
Biological Process (BP) response to alcohol 0.00007751 Highly Informative Direct
Biological Process (BP) protein targeting to nucleus 0.0001252 Highly Informative Direct
Biological Process (BP) protein import 0.0002009 Highly Informative Direct
Biological Process (BP) response to heat 0.0003605 Highly Informative Direct
Biological Process (BP) DNA integrity checkpoint 0.0004075 Highly Informative Direct
Biological Process (BP) pattern specification process 0.0004782 Highly Informative Direct
Biological Process (BP) protein methylation 0.04873 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle phase transition 0.001696 Highly Informative Inherited
Biological Process (BP) heart morphogenesis 0.006246 Highly Informative Inherited
Biological Process (BP) embryonic organ morphogenesis 0.01527 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) binding 0.09009 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.000002558 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 0 Informative Direct
Molecular Function (MF) DNA binding 0.0000000000003771 Informative Direct
Molecular Function (MF) nucleotide binding 0.00000000004817 Informative Direct
Molecular Function (MF) chromatin binding 0.00004011 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.0001177 Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.000000004738 Highly Informative Direct
Molecular Function (MF) methyltransferase activity 0.00006052 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.9619 Highly Informative Inherited
Molecular Function (MF) sequence-specific DNA binding 0.6713 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.0000001136 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.001559 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.06531 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.0000002659 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.06268 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.0000000000000368 Informative Direct
Cellular Component (CC) nucleoplasm part 0.04495 Informative Inherited
Cellular Component (CC) chromatin 0 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)Transferring one-carbon groups0.0000000003701Least InformativeDirect
Enzyme Commission (EC)Methyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.1147Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.005055Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.0147Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain development0.0009244InformativeDirect

Document: MP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)fruit0.0001209InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups0.00000000036Moderately InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processCell cycle0.9831Moderately InformativeInherited
Biological processStress response0InformativeDirect
Biological processPlant defense0InformativeDirect
Biological processMitosis0.0003642InformativeDirect
Biological processVirus entry into host cell0.001707InformativeInherited
Biological processEthylene signaling pathway0Highly InformativeDirect
Biological processViral genome integration0.0000000001024Highly InformativeDirect
Biological processDNA integration0.000004326Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Coding sequence diversityAlternative splicing0.00002843Least InformativeDirect
DomainCoiled coil0.00003524Moderately InformativeDirect
DomainBromodomain0.00000000005812Highly InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0.000000000000001107Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.000007496Moderately InformativeDirect
Post-translational modificationChromatin regulator0.000000000000708InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Fly Phenotype (FP) · Fly Anatomy (FA) · 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 5 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-binding domain 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 5 hidden Markov models representing the DNA-binding domain 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) · Mouse Phenotype (MP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]