SUPERFAMILY 1.75 HMM library and genome assignments server

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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 0.00000000002177 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.01243 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.001359 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.1182 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.1417 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.3015 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.4749 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.01246 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.01401 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.1052 Least Informative Inherited
Biological Process (BP) developmental process 0.03627 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.095 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.3667 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 0.0000000000003226 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.00000000005012 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0000002791 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0000005035 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.000001125 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.000009626 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.0000146 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.02249 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.00563 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.1055 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.2906 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.8444 Moderately Informative Inherited
Biological Process (BP) reproduction 0.003435 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.8659 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 0.03626 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.4497 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.08633 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.00106 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.01368 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.5604 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.003575 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) organ development 0.8806 Moderately Informative Inherited
Biological Process (BP) tissue development 0.3988 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.3995 Moderately Informative Inherited
Biological Process (BP) chromosome organization 0.0000000000001427 Informative Direct
Biological Process (BP) response to hormone stimulus 0.0000000000005327 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.00000005828 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.00001104 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.00002149 Informative Direct
Biological Process (BP) reproductive system development 0.00002694 Informative Direct
Biological Process (BP) response to inorganic substance 0.0001377 Informative Direct
Biological Process (BP) immune effector process 0.000236 Informative Direct
Biological Process (BP) DNA metabolic process 0.0005277 Informative Direct
Biological Process (BP) cardiovascular system development 0.8715 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.001781 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.1764 Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle 0.1873 Informative Inherited
Biological Process (BP) regulation of growth 0.02526 Informative Inherited
Biological Process (BP) protein localization to organelle 0.1227 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 1 Informative Inherited
Biological Process (BP) regulation of cell cycle process 0.04144 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.1682 Informative Inherited
Biological Process (BP) response to organonitrogen compound 0.04566 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.001926 Informative Inherited
Biological Process (BP) response to lipid 0.01175 Informative Inherited
Biological Process (BP) cell cycle process 0.07348 Informative Inherited
Biological Process (BP) protein transport 0.184 Informative Inherited
Biological Process (BP) tube development 0.3683 Informative Inherited
Biological Process (BP) organ morphogenesis 0.4141 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.4763 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.5012 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) defense response 0.3819 Informative Inherited
Biological Process (BP) embryonic organ development 0.1274 Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0.6084 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 0.000000000003069 Highly Informative Direct
Biological Process (BP) gene silencing 0.000000000005406 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.0000000001621 Highly Informative Direct
Biological Process (BP) post-embryonic development 0.0000000004147 Highly Informative Direct
Biological Process (BP) response to cold 0.0000000004474 Highly Informative Direct
Biological Process (BP) protein deacylation 0.000000006888 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.0000000105 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.00000002222 Highly Informative Direct
Biological Process (BP) DNA modification 0.0000003394 Highly Informative Direct
Biological Process (BP) internal protein amino acid acetylation 0.000001245 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.000005312 Highly Informative Direct
Biological Process (BP) response to fungus 0.00002774 Highly Informative Direct
Biological Process (BP) nuclear import 0.00002932 Highly Informative Direct
Biological Process (BP) response to alcohol 0.00007437 Highly Informative Direct
Biological Process (BP) pattern specification process 0.00007894 Highly Informative Direct
Biological Process (BP) protein localization to nucleus 0.0001031 Highly Informative Direct
Biological Process (BP) protein import 0.0001782 Highly Informative Direct
Biological Process (BP) DNA damage checkpoint 0.000241 Highly Informative Direct
Biological Process (BP) response to heat 0.0003154 Highly Informative Direct
Biological Process (BP) protein methylation 0.04008 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle phase transition 0.001297 Highly Informative Inherited
Biological Process (BP) protein targeting to nucleus 0.007214 Highly Informative Inherited
Biological Process (BP) heart morphogenesis 0.00577 Highly Informative Inherited
Biological Process (BP) embryonic organ morphogenesis 0.01284 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 0.06326 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 0.00000000003236 Informative Direct
Molecular Function (MF) DNA binding 0.00000000003544 Informative Direct
Molecular Function (MF) chromatin binding 0.00003835 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.00009734 Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.000000002609 Highly Informative Direct
Molecular Function (MF) methyltransferase activity 0.00004966 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.9623 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.0000003112 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.06591 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.001047 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.000002582 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.1407 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.0000000000001122 Informative Direct
Cellular Component (CC) nucleoplasm part 0.3099 Informative Inherited
Cellular Component (CC) chromatin 0.0001875 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 ]