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Bromodomain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Bromodomain-like [ 47363] (15)
Superfamily:   Bromodomain [ 47370]
Families:   Bromodomain [ 47371] (4)


Superfamily statistics
Genomes (502) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 13,629 33,908 8
Proteins 10,661 25,655 7


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details) Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) multicellular organismal process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0000002456 Least Informative Direct
Biological Process (BP) biological regulation 0.00000004281 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0005308 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.4306 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.2444 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.2762 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.01873 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.5082 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.9133 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.987 Least Informative Inherited
Biological Process (BP) reproduction 0.0000002269 Moderately Informative Direct
Biological Process (BP) immune system process 0.000000000001232 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.000002207 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.000000000004762 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.00000000000002273 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.00001617 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.000007462 Moderately Informative Direct
Biological Process (BP) cell differentiation 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.000000000000001925 Moderately Informative Direct
Biological Process (BP) animal organ development 0.0003697 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.00005814 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0001397 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.664 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.2144 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.873 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.1049 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.3139 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.3273 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.4236 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.988 Moderately Informative Inherited
Biological Process (BP) tissue development 0.9114 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.00884 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) single organism signaling 1 Moderately Informative Inherited
Biological Process (BP) gene expression 0.4758 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.03968 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.05954 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-templated 0.00000000000005703 Informative Direct
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.0002596 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.00000002424 Informative Direct
Biological Process (BP) positive regulation of gene expression 0.000001111 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.000000000000003734 Informative Direct
Biological Process (BP) hemopoiesis 0 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 0.0000008843 Informative Direct
Biological Process (BP) regulation of protein modification process 0.0004241 Informative Direct
Biological Process (BP) regulation of organelle organization 0.00005477 Informative Direct
Biological Process (BP) single organism reproductive process 0.0000000275 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.0002147 Informative Direct
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.0000001777 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) regulation of intracellular signal transduction 0.5619 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.1384 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.8739 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) response to radiation 0.03949 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.9299 Informative Inherited
Biological Process (BP) DNA metabolic process 0.1768 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.126 Informative Inherited
Biological Process (BP) cell development 0.1771 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 1 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.702 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.9548 Informative Inherited
Biological Process (BP) generation of neurons 1 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 0.0339 Informative Inherited
Biological Process (BP) cell cycle process 0.02895 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.1404 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.3502 Informative Inherited
Biological Process (BP) reproductive system development 0.6698 Informative Inherited
Biological Process (BP) embryo development 0.8637 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.0101 Informative Inherited
Biological Process (BP) cell cycle checkpoint 0.000796 Highly Informative Direct
Biological Process (BP) circadian rhythm 0.00008103 Highly Informative Direct
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.000000000000001925 Highly Informative Direct
Biological Process (BP) myeloid cell differentiation 0.00000000000009521 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.000006645 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.00007738 Highly Informative Direct
Biological Process (BP) macromolecule methylation 0.000614 Highly Informative Direct
Biological Process (BP) DNA methylation or demethylation 0.00001105 Highly Informative Direct
Biological Process (BP) regulation of binding 0.0003016 Highly Informative Direct
Biological Process (BP) protein-DNA complex subunit organization 0 Highly Informative Direct
Biological Process (BP) plasma membrane bounded cell projection organization 0.00007135 Highly Informative Direct
Biological Process (BP) regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 0.1424 Highly Informative Inherited
Biological Process (BP) meiotic cell cycle 0.1318 Highly Informative Inherited
Biological Process (BP) myeloid cell homeostasis 0.007417 Highly Informative Inherited
Biological Process (BP) neuron development 0.1998 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.1666 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.009801 Highly Informative Inherited
Biological Process (BP) protein alkylation 0.0144 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.001751 Highly Informative Inherited
Biological Process (BP) response to UV 0.002833 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription from RNA polymerase II promoter 0.2314 Highly Informative Inherited
Biological Process (BP) cellular component disassembly 0.0232 Highly Informative Inherited
Biological Process (BP) chromatin assembly or disassembly 0.1762 Highly Informative Inherited
Biological Process (BP) positive regulation of organelle organization 0.2029 Highly Informative Inherited
Biological Process (BP) regulation of cellular response to growth factor stimulus 0.165 Highly Informative Inherited
Biological Process (BP) protein modification by small protein conjugation 0.4604 Highly Informative Inherited
Biological Process (BP) tube morphogenesis 0.811 Highly Informative Inherited
Biological Process (BP) fertilization 0.05033 Highly Informative Inherited
Biological Process (BP) nuclear division 0.00241 Highly Informative Inherited
Biological Process (BP) embryonic organ development 0.07083 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 0.005331 Highly Informative Inherited
Molecular Function (MF) binding 0.000000008138 Least Informative Direct
Molecular Function (MF) transferase activity 0.0000003006 Least Informative Direct
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.00005668 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.001089 Moderately Informative Inherited
Molecular Function (MF) DNA binding 0.0000006199 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0 Informative Direct
Molecular Function (MF) ATPase activity 0.00000244 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.1348 Informative Inherited
Molecular Function (MF) transcription factor activity, transcription factor binding 0 Highly Informative Direct
Molecular Function (MF) chromatin binding 0 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0 Highly Informative Direct
Molecular Function (MF) S-adenosylmethionine-dependent methyltransferase activity 0.0002643 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.0000002602 Highly Informative Direct
Molecular Function (MF) ubiquitin-like protein transferase activity 0.04273 Highly Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.00001906 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.5621 Moderately Informative Inherited
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0001163 Informative Direct
Cellular Component (CC) transferase complex, transferring phosphorus-containing groups 1 Informative Inherited
Cellular Component (CC) chromatin 0.0001249 Highly Informative Direct
Cellular Component (CC) protein acetyltransferase complex 0 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.000001263 Highly Informative Direct
Cellular Component (CC) RNA polymerase II transcription factor complex 0.00000006305 Highly Informative Direct
Cellular Component (CC) peptidase complex 1 Highly Informative Inherited

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 groups0.7336Least InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0Moderately InformativeDirect
Enzyme Commission (EC)Methyltransferases0.01673Moderately InformativeInherited
Enzyme Commission (EC)Histone acetyltransferase0InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0.00000000006826InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0.0000000009872Moderately InformativeDirect
Biological processCell cycle0.00006447Moderately InformativeDirect
Biological processHost-virus interaction0.000195Moderately InformativeDirect
Biological processDifferentiation0.0003356Moderately InformativeDirect
Biological processBiological rhythms0.000000000007936InformativeDirect
Biological processMeiosis0.0000003228InformativeDirect
Biological processSporulation0.000001817InformativeDirect
Biological processNeurogenesis0.000005876InformativeDirect
Biological processSpermatogenesis0.00002094Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0.0000001889InformativeDirect
Coding sequence diversityAlternative splicing0.000009163Least InformativeDirect
Coding sequence diversityChromosomal rearrangement0.000000006544InformativeDirect
DiseaseTumor suppressor0.0000002716Moderately InformativeDirect
DiseaseMental retardation0.0001014InformativeDirect
DomainRepeat0.000001889Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
DomainZinc-finger0.0000000004503Moderately InformativeDirect
DomainBromodomain0Highly InformativeDirect
Molecular functionZinc0.0000000000001507Least InformativeDirect
Post-translational modificationTransferase0.1758Least InformativeInherited
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0.000000001314Moderately InformativeDirect
Post-translational modificationDNA-binding0.00000001214Moderately InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationAcyltransferase0.00000000000002555InformativeDirect
Post-translational modificationHelicase0.000000249InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect
Post-translational modificationUbl conjugation0.000000000001696Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001487 SSF47370 Protein matches
Abstract Bromodomains are found in a variety of mammalian, invertebrate and yeast DNA-binding proteins [PubMed1350857]. Bromodomains can interact with acetylated lysine [PubMed9175470]. In some proteins, the classical bromodomain has diverged to such an extent that parts of the region are either missing or contain an insertion (e.g., mammalian protein HRX, Caenorhabditis elegans hypothetical protein ZK783.4, yeast protein YTA7). The bromodomain may occur as a single copy, or in duplicate.

The precise function of the domain is unclear, but it may be involved in protein-protein interactions and may play a role in assembly or activity of multi-component complexes involved in transcriptional activation [PubMed7580139].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · 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 6 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 Bromodomain 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 6 hidden Markov models representing the Bromodomain 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]