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 (465) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 15,734 17,170 10
Proteins 13,526 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 1.907e-11 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.012 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.001283 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.1169 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.4741 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.1404 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.2993 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.01221 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.0135 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.09973 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.09401 Least Informative Inherited
Biological Process (BP) developmental process 0.03611 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.3534 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) response to abiotic stimulus 3.072e-13 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 0 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 1.209e-05 Moderately Informative Direct
Biological Process (BP) response to organic substance 1.01e-06 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 2.578e-07 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 1.124e-05 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 5.835e-07 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 3.926e-11 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.02073 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.00562 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.1071 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.2989 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.8413 Moderately Informative Inherited
Biological Process (BP) reproduction 0.003363 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.8533 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.03607 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.4441 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.07618 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.001053 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.01363 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.5774 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.7376 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.003141 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) organ development 0.8805 Moderately Informative Inherited
Biological Process (BP) tissue development 0.396 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.399 Moderately Informative Inherited
Biological Process (BP) immune effector process 0.0002351 Informative Direct
Biological Process (BP) DNA metabolic process 0.0005392 Informative Direct
Biological Process (BP) response to hormone stimulus 5.472e-13 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 1.217e-05 Informative Direct
Biological Process (BP) response to inorganic substance 0.0001325 Informative Direct
Biological Process (BP) negative regulation of gene expression 2.366e-05 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 4.069e-08 Informative Direct
Biological Process (BP) chromosome organization 1.454e-13 Informative Direct
Biological Process (BP) reproductive system development 2.702e-05 Informative Direct
Biological Process (BP) cardiovascular system development 0.8727 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.001808 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.1769 Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle 0.188 Informative Inherited
Biological Process (BP) regulation of growth 0.02487 Informative Inherited
Biological Process (BP) protein localization to organelle 0.1208 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 1 Informative Inherited
Biological Process (BP) regulation of cell cycle process 0.04105 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.1677 Informative Inherited
Biological Process (BP) response to organonitrogen compound 0.04724 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.00184 Informative Inherited
Biological Process (BP) response to lipid 0.01088 Informative Inherited
Biological Process (BP) response to other organism 0.01801 Informative Inherited
Biological Process (BP) cell cycle process 0.07404 Informative Inherited
Biological Process (BP) protein transport 0.185 Informative Inherited
Biological Process (BP) organ morphogenesis 0.4132 Informative Inherited
Biological Process (BP) tube development 0.3693 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.5035 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.4797 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) defense response 0.3887 Informative Inherited
Biological Process (BP) embryonic organ development 0.1282 Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0.6162 Informative Inherited
Biological Process (BP) DNA damage checkpoint 0.0002272 Highly Informative Direct
Biological Process (BP) DNA modification 3.461e-07 Highly Informative Direct
Biological Process (BP) internal protein amino acid acetylation 1.302e-06 Highly Informative Direct
Biological Process (BP) pattern specification process 8.104e-05 Highly Informative Direct
Biological Process (BP) response to heat 0.0003314 Highly Informative Direct
Biological Process (BP) response to cold 4.651e-10 Highly Informative Direct
Biological Process (BP) response to water deprivation 0 Highly Informative Direct
Biological Process (BP) response to fungus 2.899e-05 Highly Informative Direct
Biological Process (BP) hormone-mediated signaling pathway 0 Highly Informative Direct
Biological Process (BP) post-embryonic development 4.186e-10 Highly Informative Direct
Biological Process (BP) gene silencing 5.112e-12 Highly Informative Direct
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) protein import 0.0001766 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 2.223e-08 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 2.13e-10 Highly Informative Direct
Biological Process (BP) protein localization to nucleus 9.889e-05 Highly Informative Direct
Biological Process (BP) protein deacylation 6.366e-09 Highly Informative Direct
Biological Process (BP) regulation of multicellular organism growth 3.405e-12 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 1.184e-08 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 5.714e-06 Highly Informative Direct
Biological Process (BP) nuclear import 2.883e-05 Highly Informative Direct
Biological Process (BP) response to alcohol 7.211e-05 Highly Informative Direct
Biological Process (BP) protein methylation 0.03844 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle phase transition 0.001296 Highly Informative Inherited
Biological Process (BP) protein targeting to nucleus 0.007043 Highly Informative Inherited
Biological Process (BP) heart morphogenesis 0.005781 Highly Informative Inherited
Biological Process (BP) embryonic organ morphogenesis 0.01267 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) binding 0.05838 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) nucleotide binding 3.009e-11 Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 0 Informative Direct
Molecular Function (MF) DNA binding 2.833e-11 Informative Direct
Molecular Function (MF) chromatin binding 3.217e-05 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 9.159e-05 Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) methyltransferase activity 4.625e-05 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 1.9e-09 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.9517 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 2.81e-07 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.06622 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.00109 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 2.695e-06 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.1442 Moderately Informative Inherited
Cellular Component (CC) chromosome 1.083e-13 Informative Direct
Cellular Component (CC) nucleoplasm part 0.3111 Informative Inherited
Cellular Component (CC) chromatin 0.0002156 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 phenotype0.1124Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.004784Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.0142Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain development0.0008397InformativeDirect

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 groups3.685e-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 cycle0.9896Moderately InformativeInherited
Biological processStress response0InformativeDirect
Biological processPlant defense0InformativeDirect
Biological processMitosis0.0003949InformativeDirect
Biological processVirus entry into host cell0.00168InformativeInherited
Biological processEthylene signaling pathway0Highly InformativeDirect
Biological processViral genome integration1.032e-10Highly InformativeDirect
Biological processDNA integration4.337e-06Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Coding sequence diversityAlternative splicing1.128e-05Least InformativeDirect
DomainCoiled coil3.426e-05Moderately InformativeDirect
DomainBromodomain5.859e-11Highly InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor8.845e-16Moderately InformativeDirect
Post-translational modificationDevelopmental protein7.639e-06Moderately InformativeDirect
Post-translational modificationChromatin regulator6.324e-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 ]