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Arginase/deacetylase superfamily

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)
Families:   Arginase-like amidino hydrolases [ 52769] (4)
  Histone deacetylase, HDAC [ 52773] (3)


Superfamily statistics
Genomes (2,302) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 10,963 50,727 30
Proteins 10,616 49,890 30


Functional annotation
General category Metabolism
Detailed category Amino acids metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)organonitrogen compound metabolic process0.00000026350Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.089890.745Least InformativeInherited
Biological Process (BP)biological regulation0.86030.000102Least InformativeInherited
Biological Process (BP)primary metabolic process10.25Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.066281Least InformativeInherited
Biological Process (BP)biosynthetic process0.87581Least InformativeInherited
Biological Process (BP)single-organism cellular process0.19260.1253Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.35250.0000000000001817Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.0000000016540.0001131Moderately InformativeDirect
Biological Process (BP)single-organism catabolic process0.000000013650.0005286Moderately InformativeDirect
Biological Process (BP)organelle organization0.014650.000000000000005563Moderately InformativeInherited
Biological Process (BP)regulation of molecular function0.012320.4719Moderately InformativeInherited
Biological Process (BP)regulation of cellular component organization0.0039860.233Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.00038140.5906Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.000050530.4603Moderately InformativeInherited
Biological Process (BP)glutamine family amino acid metabolic process0.0000000016490.00000002843InformativeDirect
Biological Process (BP)amine metabolic process0.00000028790.000004695InformativeDirect
Biological Process (BP)regulation of organelle organization0.000042370.0006128InformativeDirect
Biological Process (BP)chromosome organization0.00000036860InformativeDirect
Biological Process (BP)carboxylic acid catabolic process0.00000051010.001732InformativeInherited
Biological Process (BP)arginine metabolic process0.0000090380.0000003876Highly InformativeDirect
Biological Process (BP)polyamine metabolic process00Highly InformativeDirect
Biological Process (BP)glutamine family amino acid catabolic process0.00000013360.00000005898Highly InformativeDirect
Biological Process (BP)regulation of chromosome organization0.000000007130.0009244Highly InformativeDirect
Biological Process (BP)regulation of binding0.000032890.000001978Highly InformativeDirect
Molecular Function (MF)hydrolase activity00Least InformativeDirect
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)metal ion binding0.02680.1656Moderately InformativeInherited
Molecular Function (MF)hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds00InformativeDirect
Molecular Function (MF)transcription factor binding0.0000065050Highly InformativeDirect
Molecular Function (MF)deacetylase activity0.0000000000094940Highly InformativeDirect
Molecular Function (MF)manganese ion binding0.00020990.000326Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.0034150.00001935Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.73360.06205Least InformativeInherited
Cellular Component (CC)nuclear part0.25370.0005127Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.046550.000000247Moderately InformativeInherited
Cellular Component (CC)nucleoplasm part0.000058010InformativeDirect
Cellular Component (CC)histone deacetylase complex0.00000000000063760Highly InformativeDirect

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) biological regulation 0.000102 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0000000000001817 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.02719 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.745 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.1253 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.25 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.2143 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.0001131 Moderately Informative Direct
Biological Process (BP) organelle organization 0.000000000000005563 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.000008437 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.000001477 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.0000000674 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0000002408 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.000002502 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.0005286 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0001683 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.0001198 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) single organism signaling 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.1119 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.1281 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.03499 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.2123 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.233 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.4719 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.7105 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.7497 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.8833 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.01662 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.452 Moderately Informative Inherited
Biological Process (BP) response to biotic stimulus 0.07709 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.9466 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.04948 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.03059 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.02977 Moderately Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0.03875 Moderately Informative Inherited
Biological Process (BP) tissue development 0.5003 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.5906 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.001411 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.2939 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.1599 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.7457 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.4603 Moderately Informative Inherited
Biological Process (BP) glutamine family amino acid metabolic process 0.00000002843 Informative Direct
Biological Process (BP) amine metabolic process 0.000004695 Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.000001281 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.00003472 Informative Direct
Biological Process (BP) electron transport chain 0.000001072 Informative Direct
Biological Process (BP) hemopoiesis 0.00001362 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.00000445 Informative Direct
Biological Process (BP) regulation of organelle organization 0.0006128 Informative Direct
Biological Process (BP) cellular respiration 0.00003642 Informative Direct
Biological Process (BP) regulation of cell differentiation 0.000000217 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.0004692 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) response to nitrogen compound 0.0003404 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.6791 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.01416 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.9324 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.006197 Informative Inherited
Biological Process (BP) response to oxidative stress 0.01743 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.01586 Informative Inherited
Biological Process (BP) epithelium development 0.6909 Informative Inherited
Biological Process (BP) system process 0.06454 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.03585 Informative Inherited
Biological Process (BP) central nervous system development 0.3667 Informative Inherited
Biological Process (BP) embryo development 0.03825 Informative Inherited
Biological Process (BP) animal organ morphogenesis 0.03451 Informative Inherited
Biological Process (BP) positive regulation of gene expression 1 Informative Inherited
Biological Process (BP) generation of neurons 0.7695 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.2263 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.002902 Informative Inherited
Biological Process (BP) behavior 0.003116 Informative Inherited
Biological Process (BP) response to wounding 0.02208 Informative Inherited
Biological Process (BP) regulation of cytokine production 0.5554 Informative Inherited
Biological Process (BP) response to bacterium 0.07983 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 1 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 0.006993 Informative Inherited
Biological Process (BP) cell activation 0.05859 Informative Inherited
Biological Process (BP) secretion by cell 0.01935 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.4276 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 0.9134 Informative Inherited
Biological Process (BP) cell development 0.2742 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.03404 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.001732 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 0.3389 Informative Inherited
Biological Process (BP) locomotion 0.1374 Informative Inherited
Biological Process (BP) localization of cell 0.04473 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.7148 Informative Inherited
Biological Process (BP) regulation of neurotransmitter levels 0.00002725 Highly Informative Direct
Biological Process (BP) citrate metabolic process 0.00000002553 Highly Informative Direct
Biological Process (BP) arginine metabolic process 0.0000003876 Highly Informative Direct
Biological Process (BP) polyamine metabolic process 0 Highly Informative Direct
Biological Process (BP) circadian rhythm 0.0004337 Highly Informative Direct
Biological Process (BP) aerobic respiration 0.000000167 Highly Informative Direct
Biological Process (BP) glutamine family amino acid catabolic process 0.00000005898 Highly Informative Direct
Biological Process (BP) gene silencing 0.000000000209 Highly Informative Direct
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.0000000000007331 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.0005829 Highly Informative Direct
Biological Process (BP) regulation of interleukin-1 production 0.000004797 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.0009244 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.000000004505 Highly Informative Direct
Biological Process (BP) response to drug 0.0002384 Highly Informative Direct
Biological Process (BP) response to hydrogen peroxide 0.0001651 Highly Informative Direct
Biological Process (BP) camera-type eye development 0.0003112 Highly Informative Direct
Biological Process (BP) pigmentation 0.0008273 Highly Informative Direct
Biological Process (BP) single-organism behavior 0.0001265 Highly Informative Direct
Biological Process (BP) regulation of binding 0.000001978 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0.00000003865 Highly Informative Direct
Biological Process (BP) response to glucocorticoid 0.0001379 Highly Informative Direct
Biological Process (BP) positive regulation of nervous system development 0.00002117 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.02635 Highly Informative Inherited
Biological Process (BP) cell-cell signaling 0.001702 Highly Informative Inherited
Biological Process (BP) response to ketone 0.008508 Highly Informative Inherited
Biological Process (BP) cellular response to reactive oxygen species 0.006429 Highly Informative Inherited
Biological Process (BP) sensory organ morphogenesis 0.009932 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 0.3634 Highly Informative Inherited
Biological Process (BP) cell proliferation 0.153 Highly Informative Inherited
Biological Process (BP) neuron development 0.8451 Highly Informative Inherited
Biological Process (BP) gliogenesis 0.004391 Highly Informative Inherited
Biological Process (BP) embryonic organ development 0.1353 Highly Informative Inherited
Biological Process (BP) positive regulation of cell development 0.003906 Highly Informative Inherited
Biological Process (BP) negative regulation of nervous system development 0.03828 Highly Informative Inherited
Biological Process (BP) regeneration 0.004812 Highly Informative Inherited
Biological Process (BP) wound healing 0.5818 Highly Informative Inherited
Biological Process (BP) response to molecule of bacterial origin 0.001072 Highly Informative Inherited
Biological Process (BP) lymphocyte activation 0.0452 Highly Informative Inherited
Biological Process (BP) leukocyte differentiation 0.01109 Highly Informative Inherited
Biological Process (BP) negative regulation of cell development 0.06527 Highly Informative Inherited
Biological Process (BP) regulation of neuron projection development 0.1205 Highly Informative Inherited
Biological Process (BP) nervous system process 0.4455 Highly Informative Inherited
Biological Process (BP) developmental growth involved in morphogenesis 0.008559 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.4293 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 0.1656 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 0 Informative Direct
Molecular Function (MF) enzyme binding 0.00002319 Informative Direct
Molecular Function (MF) DNA binding 0.02214 Informative Inherited
Molecular Function (MF) transcription factor activity, transcription factor binding 0 Highly Informative Direct
Molecular Function (MF) chromatin binding 0.000000008794 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0 Highly Informative Direct
Molecular Function (MF) deacetylase activity 0 Highly Informative Direct
Molecular Function (MF) manganese ion binding 0.000326 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.00006092 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00001935 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.06205 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.7246 Least Informative Inherited
Cellular Component (CC) nuclear part 0.0005127 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.000000247 Moderately Informative Direct
Cellular Component (CC) transferase complex 1 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.000006336 Informative Direct
Cellular Component (CC) nucleoplasm part 0 Informative Direct
Cellular Component (CC) histone deacetylase complex 0 Highly Informative Direct
Cellular Component (CC) chromatin 0.000000004134 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)In linear amides0.8808Moderately InformativeInherited
Enzyme Commission (EC)In linear amidines0Highly 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 rhythms0.000004891InformativeDirect
Biological processPolyamine biosynthesis0Highly InformativeDirect
Biological processArginine metabolism0Highly InformativeDirect
Biological processHistidine metabolism0Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
DomainTransit peptide0.0006635Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationUbl conjugation0.0000007435Moderately InformativeDirect
Post-translational modificationIsopeptide bond0.00003959Moderately InformativeDirect
Post-translational modificationS-nitrosylation0.0000001077InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · 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 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.


Browse and view proteins in genomes which have different domain combinations including a Arginase/deacetylase 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 11 hidden Markov models representing the Arginase/deacetylase 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]