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Histone deacetylase, HDAC family

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Arginase/deacetylase [ 52767]
Superfamily:   Arginase/deacetylase [ 52768] (2)
Family:   Histone deacetylase, HDAC [ 52773] (3)


Family statistics
Genomes (1,591) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 5,138 19,278 4
Proteins 4,977 18,867 4


Gene Ontology (high-quality)

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show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)biological regulation0.28660.0000003839Least InformativeInherited
Biological Process (BP)organelle organization0.00016220Moderately InformativeDirect
Biological Process (BP)regulation of molecular function0.0060410.581Moderately InformativeInherited
Biological Process (BP)regulation of organelle organization0.00000058290.0003571InformativeDirect
Biological Process (BP)chromosome organization0.000000001580InformativeDirect
Biological Process (BP)regulation of chromosome organization0.000000000038710.0003823Highly InformativeDirect
Biological Process (BP)regulation of binding0.00000014610.00000055Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.0000043990Least InformativeDirect
Molecular Function (MF)binding0.95031Least InformativeInherited
Molecular Function (MF)protein binding0.55770.1212Moderately InformativeInherited
Molecular Function (MF)hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.000000058970InformativeDirect
Molecular Function (MF)transcription factor binding0.00000019020Highly InformativeDirect
Molecular Function (MF)hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides0.010150Highly InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.068570.00004966Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.25690.003049Least InformativeInherited
Cellular Component (CC)macromolecular complex0.064620.000004038Least InformativeInherited
Cellular Component (CC)nuclear part0.043940.00005799Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.010150.000000003891Moderately InformativeInherited
Cellular Component (CC)catalytic complex0.0051390.00000000001066Moderately InformativeInherited
Cellular Component (CC)nucleoplasm part0.0000012350InformativeDirect

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) macromolecule metabolic process 0.0000000006829 Least Informative Direct
Biological Process (BP) biological regulation 0.0000003839 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.000000000005681 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.351 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.006525 Least Informative Inherited
Biological Process (BP) response to stimulus 0.9394 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) organelle organization 0 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0.00000001917 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 0.0000003279 Moderately Informative Direct
Biological Process (BP) macromolecule modification 0 Moderately Informative Direct
Biological Process (BP) cellular protein metabolic process 0 Moderately Informative Direct
Biological Process (BP) negative regulation of biological process 0.00003887 Moderately Informative Direct
Biological Process (BP) cellular developmental process 0.00000254 Moderately Informative Direct
Biological Process (BP) cellular response to stimulus 0.6546 Moderately Informative Inherited
Biological Process (BP) single-organism localization 0.647 Moderately Informative Inherited
Biological Process (BP) single organism signaling 0.9068 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.1777 Moderately Informative Inherited
Biological Process (BP) regulation of primary metabolic process 0.0292 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.004417 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.581 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.7077 Moderately Informative Inherited
Biological Process (BP) response to stress 0.01339 Moderately Informative Inherited
Biological Process (BP) response to chemical 0.6121 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) transport 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.0024 Moderately Informative Inherited
Biological Process (BP) system development 0.001923 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule metabolic process 0.009293 Moderately Informative Inherited
Biological Process (BP) carboxylic acid metabolic process 0.4466 Moderately Informative Inherited
Biological Process (BP) regulation of transcription, DNA-templated 0.0000000268 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.000002246 Informative Direct
Biological Process (BP) negative regulation of macromolecule metabolic process 0.00002039 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 0.0003139 Informative Direct
Biological Process (BP) negative regulation of cellular metabolic process 0.0000007153 Informative Direct
Biological Process (BP) regulation of organelle organization 0.0003571 Informative Direct
Biological Process (BP) regulation of cell differentiation 0.0000002025 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.000001987 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) response to nitrogen compound 0.0009138 Informative Direct
Biological Process (BP) regulation of multicellular organismal development 0.0009381 Informative Direct
Biological Process (BP) cell surface receptor signaling pathway 0.786 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.01426 Informative Inherited
Biological Process (BP) secretion 0.01143 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.8913 Informative Inherited
Biological Process (BP) system process 0.06572 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.03488 Informative Inherited
Biological Process (BP) embryo development 0.01822 Informative Inherited
Biological Process (BP) behavior 0.001043 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.0226 Informative Inherited
Biological Process (BP) response to oxidative stress 0.02282 Informative Inherited
Biological Process (BP) regulation of cytokine production 0.511 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 1 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 1 Informative Inherited
Biological Process (BP) growth 0.001859 Informative Inherited
Biological Process (BP) cell activation 0.04399 Informative Inherited
Biological Process (BP) tissue development 0.4988 Informative Inherited
Biological Process (BP) nervous system development 0.01258 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.2778 Informative Inherited
Biological Process (BP) cell development 0.1595 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.02735 Informative Inherited
Biological Process (BP) defense response 0.7018 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 0.077 Informative Inherited
Biological Process (BP) locomotion 0.06662 Informative Inherited
Biological Process (BP) citrate metabolic process 0.0000000115 Highly Informative Direct
Biological Process (BP) inflammatory response 0.000516 Highly Informative Direct
Biological Process (BP) cell-cell signaling 0.0001546 Highly Informative Direct
Biological Process (BP) aerobic respiration 0.00000006704 Highly Informative Direct
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.000000000000005999 Highly Informative Direct
Biological Process (BP) respiratory electron transport chain 0.00000001561 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.0002373 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.0003823 Highly Informative Direct
Biological Process (BP) camera-type eye development 0.0001291 Highly Informative Direct
Biological Process (BP) single-organism behavior 0.00001993 Highly Informative Direct
Biological Process (BP) negative regulation of nucleobase-containing compound metabolic process 0.0000002691 Highly Informative Direct
Biological Process (BP) lymphocyte activation 0.000516 Highly Informative Direct
Biological Process (BP) regulation of neurogenesis 0.0003703 Highly Informative Direct
Biological Process (BP) regulation of binding 0.00000055 Highly Informative Direct
Biological Process (BP) negative regulation of cellular macromolecule biosynthetic process 0.00002012 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.02342 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 0.2054 Highly Informative Inherited
Biological Process (BP) positive regulation of cell differentiation 0.01518 Highly Informative Inherited
Biological Process (BP) cell proliferation 0.07137 Highly Informative Inherited
Biological Process (BP) neuron differentiation 0.2858 Highly Informative Inherited
Biological Process (BP) gliogenesis 0.004687 Highly Informative Inherited
Biological Process (BP) animal organ morphogenesis 0.04389 Highly Informative Inherited
Biological Process (BP) embryonic organ development 0.1028 Highly Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.05827 Highly Informative Inherited
Biological Process (BP) tube development 0.3755 Highly Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.008901 Highly Informative Inherited
Biological Process (BP) wound healing 0.1159 Highly Informative Inherited
Biological Process (BP) rhythmic process 0.001222 Highly Informative Inherited
Biological Process (BP) negative regulation of organelle organization 0.08706 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription, DNA-templated 1 Highly Informative Inherited
Biological Process (BP) leukocyte differentiation 0.01141 Highly Informative Inherited
Biological Process (BP) brain development 0.1183 Highly Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.08673 Highly Informative Inherited
Biological Process (BP) regulation of cell projection organization 0.07114 Highly Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.001906 Highly Informative Inherited
Biological Process (BP) nervous system process 0.2403 Highly Informative Inherited
Biological Process (BP) developmental growth involved in morphogenesis 0.00685 Highly Informative Inherited
Biological Process (BP) cell migration 0.01197 Highly Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.763 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) protein binding 0.1212 Moderately Informative Inherited
Molecular Function (MF) organic cyclic compound binding 0.7429 Moderately Informative Inherited
Molecular Function (MF) heterocyclic compound binding 0.7021 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 0 Informative Direct
Molecular Function (MF) enzyme binding 0.00003238 Informative Direct
Molecular Function (MF) DNA binding 0.006491 Informative Inherited
Molecular Function (MF) chromatin binding 0.000000001007 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0 Highly Informative Direct
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.00001689 Highly Informative Direct
Cellular Component (CC) macromolecular complex 0.000004038 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00004966 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.003049 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.2689 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00005799 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.000000003891 Moderately Informative Direct
Cellular Component (CC) catalytic complex 0.00000000001066 Moderately Informative Direct
Cellular Component (CC) chromosome 0.0000002953 Informative Direct
Cellular Component (CC) nucleoplasm part 0 Informative Direct
Cellular Component (CC) chromatin 0.0000000001777 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)Acting on carbon-nitrogen bonds, other than peptid0Moderately InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processBiological rhythms0.000000006004InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Coding sequence diversityAlternative splicing0.0000000006512Least InformativeDirect
Molecular functionZinc0.0000007926Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationPhosphoprotein0.0000000007411Least InformativeDirect
Post-translational modificationUbl conjugation0.000000000009772Moderately InformativeDirect
Post-translational modificationIsopeptide bond0.000000057Moderately InformativeDirect
Post-translational modificationS-nitrosylation0.000000006049InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

   
Superfamily level     Family level

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.


   
Superfamily level     Family level

Alignments of sequences to 11 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.


Superfamily level

Browse and view proteins in genomes which have different domain combinations including a Arginase/deacetylase domain.


   
Superfamily level     Family level

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.


Jump to [ Top of page · SCOP classification · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]