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 (430) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 11,556 10,632 10
Proteins 9,888 9,680 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 1.234e-11 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.01603 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.003913 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.1205 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.1434 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.3046 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.4663 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.04292 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.05332 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.1691 Least Informative Inherited
Biological Process (BP) developmental process 0.03017 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.07877 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.563 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) regulation of cellular biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 2.518e-13 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 4.839e-11 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 5.518e-07 Moderately Informative Direct
Biological Process (BP) response to organic substance 8.291e-07 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1.492e-06 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 3.839e-05 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 5.084e-05 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.01959 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.1053 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.2999 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.7748 Moderately Informative Inherited
Biological Process (BP) reproduction 0.003181 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.7714 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.002246 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.03404 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.2788 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.1247 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.003019 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.01375 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.0206 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.5498 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.7202 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.002183 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) organ development 0.8429 Moderately Informative Inherited
Biological Process (BP) tissue development 0.3781 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.3475 Moderately Informative Inherited
Biological Process (BP) response to hormone stimulus 4.472e-13 Informative Direct
Biological Process (BP) chromosome organization 3.596e-12 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 2.58e-07 Informative Direct
Biological Process (BP) reproductive structure development 7.449e-06 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 4.595e-05 Informative Direct
Biological Process (BP) negative regulation of gene expression 8.336e-05 Informative Direct
Biological Process (BP) response to inorganic substance 0.0001347 Informative Direct
Biological Process (BP) DNA metabolic process 0.0002196 Informative Direct
Biological Process (BP) immune effector process 0.0002546 Informative Direct
Biological Process (BP) cardiovascular system development 0.8907 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.001802 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.187 Informative Inherited
Biological Process (BP) regulation of growth 0.02004 Informative Inherited
Biological Process (BP) protein localization to organelle 0.1381 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 1 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.965 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.4866 Informative Inherited
Biological Process (BP) protein transport 0.1831 Informative Inherited
Biological Process (BP) response to organonitrogen compound 0.04715 Informative Inherited
Biological Process (BP) response to lipid 0.01109 Informative Inherited
Biological Process (BP) cell cycle process 0.07474 Informative Inherited
Biological Process (BP) organ morphogenesis 0.3938 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.461 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.5034 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) defense response 0.3747 Informative Inherited
Biological Process (BP) embryonic organ development 0.1246 Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0.6302 Informative Inherited
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) histone modification 3.746e-15 Highly Informative Direct
Biological Process (BP) gene silencing 3.876e-12 Highly Informative Direct
Biological Process (BP) regulation of multicellular organism growth 5.649e-12 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 1.163e-10 Highly Informative Direct
Biological Process (BP) post-embryonic development 2.122e-10 Highly Informative Direct
Biological Process (BP) response to cold 8.258e-10 Highly Informative Direct
Biological Process (BP) protein deacylation 9.712e-10 Highly Informative Direct
Biological Process (BP) chromatin assembly 1.904e-09 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 1.971e-08 Highly Informative Direct
Biological Process (BP) DNA modification 1.31e-07 Highly Informative Direct
Biological Process (BP) internal protein amino acid acetylation 1.256e-06 Highly Informative Direct
Biological Process (BP) response to osmotic stress 2.477e-06 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 1.628e-05 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 1.919e-05 Highly Informative Direct
Biological Process (BP) nuclear import 3.354e-05 Highly Informative Direct
Biological Process (BP) response to fungus 3.731e-05 Highly Informative Direct
Biological Process (BP) pattern specification process 9.449e-05 Highly Informative Direct
Biological Process (BP) protein localization to nucleus 0.0001128 Highly Informative Direct
Biological Process (BP) protein import 0.000191 Highly Informative Direct
Biological Process (BP) response to heat 0.0003334 Highly Informative Direct
Biological Process (BP) protein methylation 0.08674 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle phase transition 0.001099 Highly Informative Inherited
Biological Process (BP) protein targeting to nucleus 0.007438 Highly Informative Inherited
Biological Process (BP) cell cycle checkpoint 0.002546 Highly Informative Inherited
Biological Process (BP) epithelial tube morphogenesis 0.03441 Highly Informative Inherited
Biological Process (BP) heart morphogenesis 0.005194 Highly Informative Inherited
Biological Process (BP) embryonic organ morphogenesis 0.01246 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) binding 0.5262 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 1.972e-11 Informative Direct
Molecular Function (MF) DNA binding 4.327e-09 Informative Direct
Molecular Function (MF) chromatin binding 4.654e-06 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 9.011e-05 Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) S-adenosylmethionine-dependent methyltransferase activity 6.467e-06 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.6658 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1.745e-07 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.204 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.003248 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 3.878e-06 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.1956 Moderately Informative Inherited
Cellular Component (CC) chromosome 5.405e-12 Informative Direct
Cellular Component (CC) nucleolus 3.331e-09 Informative Direct
Cellular Component (CC) nucleoplasm part 0.3272 Informative Inherited
Cellular Component (CC) histone deacetylase complex 9.194e-09 Highly Informative Direct
Cellular Component (CC) chromatin 0.0006259 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)cellular phenotype0.02071Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.1105Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.004655Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.01363Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain development0.0008191InformativeDirect

Document: MP 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 groups4.061e-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 cycle0.9905Moderately InformativeInherited
Biological processStress response0InformativeDirect
Biological processPlant defense0InformativeDirect
Biological processMitosis0.0004026InformativeDirect
Biological processVirus entry into host cell0.001715InformativeInherited
Biological processEthylene signaling pathway0Highly InformativeDirect
Biological processViral genome integration1.066e-10Highly InformativeDirect
Biological processDNA integration4.253e-06Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Coding sequence diversityAlternative splicing7.094e-06Least InformativeDirect
DomainCoiled coil3.199e-05Moderately InformativeDirect
DomainBromodomain5.79e-11Highly InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor6.651e-16Moderately InformativeDirect
Post-translational modificationDevelopmental protein7.685e-06Moderately InformativeDirect
Post-translational modificationChromatin regulator5.679e-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 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 Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]