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 (456) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 14,369 17,170 10
Proteins 12,302 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 1.724e-12 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0006752 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.01341 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.08372 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.1023 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.2414 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.4735 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.007138 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.009045 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.1068 Least Informative Inherited
Biological Process (BP) developmental process 0.02168 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.06037 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.2657 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) response to endogenous stimulus 0 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 2.499e-13 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 4.527e-11 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 4.294e-09 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 2.756e-07 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 6.076e-07 Moderately Informative Direct
Biological Process (BP) response to organic substance 6.36e-07 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 1.002e-05 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.02013 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.005489 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.1017 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.3075 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.8377 Moderately Informative Inherited
Biological Process (BP) reproduction 0.002283 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.8559 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.001908 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.02755 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.4324 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.07281 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.001123 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.01062 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.5838 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.7344 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.001637 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) organ development 0.8795 Moderately Informative Inherited
Biological Process (BP) tissue development 0.3906 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.3555 Moderately Informative Inherited
Biological Process (BP) chromosome organization 1.534e-13 Informative Direct
Biological Process (BP) response to hormone stimulus 3.432e-13 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 3.926e-08 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 1.124e-05 Informative Direct
Biological Process (BP) reproductive system development 2.286e-05 Informative Direct
Biological Process (BP) response to inorganic substance 0.0001358 Informative Direct
Biological Process (BP) immune effector process 0.0001891 Informative Direct
Biological Process (BP) DNA metabolic process 0.0005634 Informative Direct
Biological Process (BP) cardiovascular system development 0.8766 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.001812 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.1759 Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle 0.1771 Informative Inherited
Biological Process (BP) regulation of growth 0.02457 Informative Inherited
Biological Process (BP) protein localization to organelle 0.1297 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 1 Informative Inherited
Biological Process (BP) regulation of cell cycle process 0.04083 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.1611 Informative Inherited
Biological Process (BP) response to organonitrogen compound 0.05268 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.001731 Informative Inherited
Biological Process (BP) response to lipid 0.01157 Informative Inherited
Biological Process (BP) response to other organism 0.01819 Informative Inherited
Biological Process (BP) cell cycle process 0.07874 Informative Inherited
Biological Process (BP) protein transport 0.18 Informative Inherited
Biological Process (BP) tube development 0.3759 Informative Inherited
Biological Process (BP) organ morphogenesis 0.4203 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.4728 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.5004 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) defense response 0.3901 Informative Inherited
Biological Process (BP) embryonic organ development 0.129 Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0.6206 Informative Inherited
Biological Process (BP) response to water deprivation 0 Highly Informative Direct
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) hormone-mediated signaling pathway 0 Highly Informative Direct
Biological Process (BP) regulation of multicellular organism growth 3.713e-12 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 1.241e-10 Highly Informative Direct
Biological Process (BP) post-embryonic development 1.734e-10 Highly Informative Direct
Biological Process (BP) response to cold 5.698e-10 Highly Informative Direct
Biological Process (BP) chromatin assembly 1.625e-09 Highly Informative Direct
Biological Process (BP) protein deacylation 6.254e-09 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 8.475e-09 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 1.384e-08 Highly Informative Direct
Biological Process (BP) DNA modification 3.25e-07 Highly Informative Direct
Biological Process (BP) internal protein amino acid acetylation 9.192e-07 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 5.096e-06 Highly Informative Direct
Biological Process (BP) nuclear import 2.41e-05 Highly Informative Direct
Biological Process (BP) response to fungus 3.303e-05 Highly Informative Direct
Biological Process (BP) protein localization to nucleus 8.145e-05 Highly Informative Direct
Biological Process (BP) pattern specification process 8.663e-05 Highly Informative Direct
Biological Process (BP) protein import 0.000145 Highly Informative Direct
Biological Process (BP) DNA damage checkpoint 0.0001932 Highly Informative Direct
Biological Process (BP) response to heat 0.0003425 Highly Informative Direct
Biological Process (BP) protein methylation 0.03971 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle phase transition 0.001028 Highly Informative Inherited
Biological Process (BP) protein targeting to nucleus 0.007035 Highly Informative Inherited
Biological Process (BP) heart morphogenesis 0.004872 Highly Informative Inherited
Biological Process (BP) embryonic organ morphogenesis 0.01125 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) binding 0.3657 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 0 Informative Direct
Molecular Function (MF) nucleotide binding 1.576e-11 Informative Direct
Molecular Function (MF) DNA binding 1.702e-09 Informative Direct
Molecular Function (MF) chromatin binding 7.767e-06 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 6.75e-05 Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) methyltransferase activity 3.384e-05 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.7397 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 7.882e-08 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.07296 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.001051 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 3.316e-06 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.1597 Moderately Informative Inherited
Cellular Component (CC) chromosome 7.862e-14 Informative Direct
Cellular Component (CC) nucleoplasm part 0.2943 Informative Inherited
Cellular Component (CC) histone deacetylase complex 6.448e-09 Highly Informative Direct
Cellular Component (CC) SWI/SNF superfamily-type complex 1.092e-05 Highly Informative Direct
Cellular Component (CC) chromatin 0.000219 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 groups3.701e-10Least 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 phenotype0.1131Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.004876Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.01422Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain development0.0008542InformativeDirect

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 groups3.708e-10Moderately 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 cycle0.9904Moderately InformativeInherited
Biological processStress response0InformativeDirect
Biological processPlant defense0InformativeDirect
Biological processMitosis0.0003977InformativeDirect
Biological processVirus entry into host cell0.001684InformativeInherited
Biological processEthylene signaling pathway0Highly InformativeDirect
Biological processViral genome integration1.003e-10Highly InformativeDirect
Biological processDNA integration4.223e-06Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Coding sequence diversityAlternative splicing1.13e-05Least InformativeDirect
DomainCoiled coil3.444e-05Moderately InformativeDirect
DomainBromodomain5.92e-11Highly InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor8.838e-16Moderately InformativeDirect
Post-translational modificationDevelopmental protein7.767e-06Moderately InformativeDirect
Post-translational modificationChromatin regulator6.465e-13InformativeDirect

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 ]