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SET domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   beta-clip [ 51268] (7)
Superfamily:   SET domain [ 82199] (3)
Families:   Histone lysine methyltransferases [ 82200] (3)
  Viral histone H3 Lysine 27 Methyltransferase [ 82207]
  RuBisCo LSMT catalytic domain [ 82210]


Superfamily statistics
Genomes (940) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 18,958 46,720 13
Proteins 18,582 45,815 13


Functional annotation
General category Processes_IC
Detailed category Ion 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)multicellular organismal process0.000025680.0000001652Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.30520Least InformativeInherited
Biological Process (BP)primary metabolic process0.79170.00000000000008578Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.48230Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.033160Least InformativeInherited
Biological Process (BP)immune system process0.018950.7883Moderately InformativeInherited
Biological Process (BP)animal organ development0.47760.04441Moderately InformativeInherited
Biological Process (BP)organelle organization0.076640Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.019110Moderately InformativeInherited
Biological Process (BP)hemopoiesis0.000061810.00003303InformativeDirect
Biological Process (BP)chromosome organization0.0029670InformativeInherited
Biological Process (BP)protein alkylation0.0000022220Highly InformativeDirect
Biological Process (BP)histone modification0.0000024580Highly InformativeDirect
Biological Process (BP)macromolecule methylation0.000018140Highly 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) multicellular organismal process 0.0000001652 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.00000000000008578 Least Informative Direct
Biological Process (BP) biological regulation 0.00000000000002436 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.0000000000006985 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.000002687 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.00000000009024 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.000009293 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.1262 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.07159 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.3179 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) protein complex biogenesis 0.2937 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.04441 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.7837 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.09795 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 1 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) cell differentiation 0.1179 Moderately Informative Inherited
Biological Process (BP) immune system process 0.7883 Moderately Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.000006286 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.00000000001941 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0 Informative Direct
Biological Process (BP) hemopoiesis 0.00003303 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.000000001527 Informative Direct
Biological Process (BP) regulation of protein modification process 0.000008121 Informative Direct
Biological Process (BP) regulation of organelle organization 0.000000000000003734 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.04517 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.01541 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.3839 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 1 Informative Inherited
Biological Process (BP) supramolecular fiber organization 0.5524 Informative Inherited
Biological Process (BP) cell development 0.7156 Informative Inherited
Biological Process (BP) system process 1 Informative Inherited
Biological Process (BP) embryo development 0.08664 Informative Inherited
Biological Process (BP) animal organ morphogenesis 0.4001 Informative Inherited
Biological Process (BP) generation of neurons 1 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.2686 Informative Inherited
Biological Process (BP) actin cytoskeleton organization 0.2257 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.01505 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.9943 Informative Inherited
Biological Process (BP) cellular response to lipid 0.0415 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.1795 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 1 Informative Inherited
Biological Process (BP) cellular protein complex assembly 0.01081 Informative Inherited
Biological Process (BP) organelle assembly 1 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) cellular component morphogenesis 1 Informative Inherited
Biological Process (BP) behavior 0.02583 Informative Inherited
Biological Process (BP) circulatory system development 0.004888 Informative Inherited
Biological Process (BP) DNA metabolic process 1 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 1 Informative Inherited
Biological Process (BP) myeloid cell homeostasis 0.0000002452 Highly Informative Direct
Biological Process (BP) heart development 0.00002221 Highly Informative Direct
Biological Process (BP) protein alkylation 0 Highly Informative Direct
Biological Process (BP) gene silencing 0.0000000000002512 Highly Informative Direct
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.00000000000004577 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.000000000003808 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0.000712 Highly Informative Direct
Biological Process (BP) macromolecule methylation 0 Highly Informative Direct
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 0.0000848 Highly Informative Direct
Biological Process (BP) single-organism behavior 0.000738 Highly Informative Direct
Biological Process (BP) DNA methylation or demethylation 0.00000000004499 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0.00000001365 Highly Informative Direct
Biological Process (BP) striated muscle cell development 0.0007482 Highly Informative Direct
Biological Process (BP) response to alcohol 0.0000019 Highly Informative Direct
Biological Process (BP) regulation of hemopoiesis 0.000000999 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.002604 Highly Informative Inherited
Biological Process (BP) positive regulation of organelle organization 0.00363 Highly Informative Inherited
Biological Process (BP) myeloid cell differentiation 0.006051 Highly Informative Inherited
Biological Process (BP) nervous system process 0.1663 Highly Informative Inherited
Biological Process (BP) embryonic organ development 0.005029 Highly Informative Inherited
Biological Process (BP) actomyosin structure organization 0.001102 Highly Informative Inherited
Biological Process (BP) regulation of DNA metabolic process 0.02546 Highly Informative Inherited
Biological Process (BP) neuron development 1 Highly Informative Inherited
Biological Process (BP) regulation of reproductive process 0.01007 Highly Informative Inherited
Biological Process (BP) response to ketone 0.00181 Highly Informative Inherited
Biological Process (BP) cellular component assembly involved in morphogenesis 0.005992 Highly Informative Inherited
Biological Process (BP) actin filament organization 0.003278 Highly Informative Inherited
Biological Process (BP) gliogenesis 0.05902 Highly Informative Inherited
Biological Process (BP) locomotory behavior 0.188 Highly Informative Inherited
Biological Process (BP) sensory organ morphogenesis 0.1083 Highly Informative Inherited
Molecular Function (MF) transferase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.3763 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.005249 Moderately Informative Inherited
Molecular Function (MF) DNA binding 0.00006228 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0 Informative Direct
Molecular Function (MF) enzyme binding 0.00000006078 Informative Direct
Molecular Function (MF) macromolecular complex binding 0.01122 Informative Inherited
Molecular Function (MF) transcription factor activity, transcription factor binding 0.000000001875 Highly Informative Direct
Molecular Function (MF) chromatin binding 0 Highly Informative Direct
Molecular Function (MF) S-adenosylmethionine-dependent methyltransferase activity 0.00000001091 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000000000001309 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0006573 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.3784 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00000002484 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.000000001243 Moderately Informative Direct
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.00004073 Informative Direct
Cellular Component (CC) chromatin 0.00001236 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.0002119 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 groups0Least InformativeDirect
Enzyme Commission (EC)Methyltransferases0Moderately 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 processDifferentiation0.0000000005648Moderately InformativeDirect
Biological processCell cycle0.00000003739Moderately InformativeDirect
Biological processBiological rhythms0InformativeDirect
Biological processMitosis0.00000000002005InformativeDirect
Biological processMeiosis0.000000681InformativeDirect
Biological processMyogenesis0.00000000000805Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Cellular componentCentromere0Highly InformativeDirect
Coding sequence diversityAlternative splicing0.000002862Least InformativeDirect
DomainRepeat0.0000003523Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainCoiled coil0.00000000006588Moderately InformativeDirect
DomainBromodomain0.0000002414Highly InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionS-adenosyl-L-methionine0InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.0000004194Moderately InformativeDirect
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationMethyltransferase0InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect

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 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 SET 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 SET 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]