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Radical SAM enzymes superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   TIM beta/alpha-barrel [ 51350] (33)
Superfamily:   Radical SAM enzymes [ 102114] (3)
Families:   Biotin synthase [ 102115]
  Oxygen-independent coproporphyrinogen III oxidase HemN [ 102118]
  MoCo biosynthesis proteins [ 110388]


Superfamily statistics
Genomes (3,185) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 46,002 277,822 3
Proteins 45,731 275,911 3


Functional annotation
General category Metabolism
Detailed category Other enzymes

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)cellular aromatic compound metabolic process0.00054880.0001279Least InformativeDirect
Biological Process (BP)biosynthetic process00Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.00000050430.0000001839Least InformativeDirect
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process00Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.0000000075360.00000009597Least InformativeDirect
Biological Process (BP)primary metabolic process11Least InformativeInherited
Biological Process (BP)macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)multicellular organismal process11Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.0092980.009318Least InformativeInherited
Biological Process (BP)single-organism cellular process0.31991Least InformativeInherited
Biological Process (BP)response to stimulus11Least InformativeInherited
Biological Process (BP)biological regulation11Least InformativeInherited
Biological Process (BP)heterocycle biosynthetic process00Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.0000000052920.000002572Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process00Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process00Moderately InformativeDirect
Biological Process (BP)regulation of multicellular organismal process0.22661Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process0.68871Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process0.084150.1318Moderately InformativeInherited
Biological Process (BP)response to biotic stimulus0.079590.4872Moderately InformativeInherited
Biological Process (BP)defense response0.2390.4516Moderately InformativeInherited
Biological Process (BP)animal organ development0.3931Moderately InformativeInherited
Biological Process (BP)cell differentiation0.41091Moderately InformativeInherited
Biological Process (BP)immune system process0.44021Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process0.80711Moderately InformativeInherited
Biological Process (BP)regulation of signaling0.24911Moderately InformativeInherited
Biological Process (BP)regulation of cell communication0.24851Moderately InformativeInherited
Biological Process (BP)multi-organism process0.85071Moderately InformativeInherited
Biological Process (BP)response to external stimulus0.076861Moderately InformativeInherited
Biological Process (BP)cell communication11Moderately InformativeInherited
Biological Process (BP)cellular response to stress0.05341Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.01220.009359Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.0024990.0002385Moderately InformativeInherited
Biological Process (BP)lipid metabolic process11Moderately InformativeInherited
Biological Process (BP)organophosphate biosynthetic process0.1540.001119Moderately InformativeInherited
Biological Process (BP)regulation of response to stimulus0.53431Moderately InformativeInherited
Biological Process (BP)regulation of localization0.21430.9573Moderately InformativeInherited
Biological Process (BP)tetrapyrrole metabolic process00InformativeDirect
Biological Process (BP)water-soluble vitamin biosynthetic process0.0000017870.0000000203InformativeDirect
Biological Process (BP)pigment metabolic process0.000000000000034650.000000000000131InformativeDirect
Biological Process (BP)monocarboxylic acid biosynthetic process0.00050590.00001976InformativeDirect
Biological Process (BP)regulation of protein localization0.00310.2739InformativeInherited
Biological Process (BP)immune effector process0.0020250.06934InformativeInherited
Biological Process (BP)defense response to other organism0.014340.1813InformativeInherited
Biological Process (BP)negative regulation of transport0.00015620.02207InformativeInherited
Biological Process (BP)regulation of secretion0.0017880.1313InformativeInherited
Biological Process (BP)cell activation0.0017350.1067InformativeInherited
Biological Process (BP)hemopoiesis0.00027180.07223InformativeInherited
Biological Process (BP)positive regulation of signal transduction0.013430.7974InformativeInherited
Biological Process (BP)regulation of immune response0.0040640.319InformativeInherited
Biological Process (BP)regulation of defense response0.0043010.1733InformativeInherited
Biological Process (BP)positive regulation of immune system process0.0039280.2427InformativeInherited
Biological Process (BP)cellular response to DNA damage stimulus0.00033160.1109InformativeInherited
Biological Process (BP)response to extracellular stimulus0.15540.4479InformativeInherited
Biological Process (BP)fatty acid metabolic process0.059050.02705InformativeInherited
Biological Process (BP)coenzyme biosynthetic process0.85650.2194InformativeInherited
Biological Process (BP)sulfur compound biosynthetic process0.0032910.000112InformativeInherited
Biological Process (BP)regulation of peptide transport0.0014460.1347InformativeInherited
Biological Process (BP)positive regulation of multicellular organismal process0.016181InformativeInherited
Biological Process (BP)regulation of cytokine production0.00024990.06286InformativeInherited
Biological Process (BP)positive regulation of immune effector process0.00000012180.0002019Highly InformativeDirect
Biological Process (BP)regulation of production of molecular mediator of immune response0.00000068810.000219Highly InformativeDirect
Biological Process (BP)regulation of leukocyte mediated immunity0.000000049270.0001496Highly InformativeDirect
Biological Process (BP)negative regulation of peptide secretion0.00000013220.00002735Highly InformativeDirect
Biological Process (BP)positive regulation of adaptive immune response based on somatic recombination of immune receptors b0.0000000013350.000003861Highly InformativeDirect
Biological Process (BP)biotin metabolic process0.000043050.000002447Highly InformativeDirect
Biological Process (BP)heme biosynthetic process0.000000000000029080.00000000000001763Highly InformativeDirect
Biological Process (BP)response to virus0.0000033590.0003184Highly InformativeDirect
Biological Process (BP)regulation of toll-like receptor signaling pathway0.000000000060950.0000001309Highly InformativeDirect
Biological Process (BP)negative regulation of secretion by cell0.00000068810.000224Highly InformativeDirect
Biological Process (BP)negative regulation of establishment of protein localization0.0000018270.00042Highly InformativeDirect
Biological Process (BP)lymphocyte activation0.00000082660.003602Highly InformativeInherited
Biological Process (BP)leukocyte differentiation0.00000038040.001961Highly InformativeInherited
Biological Process (BP)cellular response to extracellular stimulus0.006930.1186Highly InformativeInherited
Biological Process (BP)Mo-molybdopterin cofactor metabolic process0.0000000000012560.3329Highly InformativeInherited
Biological Process (BP)positive regulation of cytokine production0.000031520.006051Highly InformativeInherited
Molecular Function (MF)binding0.059821Least InformativeInherited
Molecular Function (MF)transferase activity10.8603Least InformativeInherited
Molecular Function (MF)oxidoreductase activity0.000020260.0006757Moderately InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.68151Moderately InformativeInherited
Molecular Function (MF)transferase activity, transferring sulfur-containing groups0.00000000086220InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity0.010510.01842InformativeInherited
Molecular Function (MF)ligase activity0.06240.1525InformativeInherited
Molecular Function (MF)oxidoreductase activity, acting on the CH-CH group of donors00Highly InformativeDirect
Molecular Function (MF)iron-sulfur cluster binding10Highly InformativeInherited
Molecular Function (MF)sulfurtransferase activity0.00000000000013580.009481Highly InformativeInherited
Cellular Component (CC)non-membrane-bounded organelle0.81641Least InformativeInherited
Cellular Component (CC)lipid droplet0.00000015340.0000006809Highly 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) cellular aromatic compound metabolic process 0.0001279 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0000001839 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.00000009597 Least Informative Direct
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.009318 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.0002385 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.000002572 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.1318 Moderately Informative Inherited
Biological Process (BP) response to biotic stimulus 0.4872 Moderately Informative Inherited
Biological Process (BP) defense response 0.4516 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) immune system process 1 Moderately Informative Inherited
Biological Process (BP) gene expression 0.1258 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.009359 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.4258 Moderately Informative Inherited
Biological Process (BP) organophosphate biosynthetic process 0.001119 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.9573 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 1 Moderately Informative Inherited
Biological Process (BP) tRNA metabolic process 0.0000032 Informative Direct
Biological Process (BP) RNA modification 0.000000161 Informative Direct
Biological Process (BP) tetrapyrrole metabolic process 0 Informative Direct
Biological Process (BP) ncRNA processing 0.00005825 Informative Direct
Biological Process (BP) water-soluble vitamin biosynthetic process 0.0000000203 Informative Direct
Biological Process (BP) pigment metabolic process 0.000000000000131 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0.000112 Informative Direct
Biological Process (BP) monocarboxylic acid biosynthetic process 0.00001976 Informative Direct
Biological Process (BP) regulation of protein localization 0.2739 Informative Inherited
Biological Process (BP) regulation of transferase activity 0.1672 Informative Inherited
Biological Process (BP) immune effector process 0.06934 Informative Inherited
Biological Process (BP) defense response to other organism 0.1813 Informative Inherited
Biological Process (BP) negative regulation of transport 0.02207 Informative Inherited
Biological Process (BP) regulation of secretion 0.1313 Informative Inherited
Biological Process (BP) cell activation 0.1067 Informative Inherited
Biological Process (BP) hemopoiesis 0.07223 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.7974 Informative Inherited
Biological Process (BP) regulation of immune response 0.319 Informative Inherited
Biological Process (BP) regulation of defense response 0.1733 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.2427 Informative Inherited
Biological Process (BP) cellular response to DNA damage stimulus 0.1109 Informative Inherited
Biological Process (BP) response to extracellular stimulus 0.4479 Informative Inherited
Biological Process (BP) fatty acid metabolic process 0.02705 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0.2194 Informative Inherited
Biological Process (BP) regulation of peptide transport 0.1347 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 1 Informative Inherited
Biological Process (BP) regulation of cytokine production 0.06286 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.908 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.7406 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.617 Informative Inherited
Biological Process (BP) positive regulation of immune effector process 0.0002019 Highly Informative Direct
Biological Process (BP) regulation of production of molecular mediator of immune response 0.000219 Highly Informative Direct
Biological Process (BP) regulation of leukocyte mediated immunity 0.0001496 Highly Informative Direct
Biological Process (BP) negative regulation of peptide secretion 0.00002735 Highly Informative Direct
Biological Process (BP) positive regulation of adaptive immune response based on somatic recombination of immune receptors b 0.000003861 Highly Informative Direct
Biological Process (BP) tRNA modification 0.0000000002555 Highly Informative Direct
Biological Process (BP) biotin metabolic process 0.000002447 Highly Informative Direct
Biological Process (BP) heme biosynthetic process 0.00000000000001763 Highly Informative Direct
Biological Process (BP) response to virus 0.0003184 Highly Informative Direct
Biological Process (BP) regulation of toll-like receptor signaling pathway 0.0000001309 Highly Informative Direct
Biological Process (BP) negative regulation of secretion by cell 0.000224 Highly Informative Direct
Biological Process (BP) negative regulation of establishment of protein localization 0.00042 Highly Informative Direct
Biological Process (BP) lymphocyte activation 0.003602 Highly Informative Inherited
Biological Process (BP) leukocyte differentiation 0.001961 Highly Informative Inherited
Biological Process (BP) cellular response to extracellular stimulus 0.1186 Highly Informative Inherited
Biological Process (BP) Mo-molybdopterin cofactor metabolic process 0.3329 Highly Informative Inherited
Biological Process (BP) positive regulation of cytokine production 0.006051 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 0.8603 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0.0006757 Moderately Informative Direct
Molecular Function (MF) molecular function regulator 0.06026 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) isomerase activity 0.02976 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring sulfur-containing groups 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.01842 Informative Inherited
Molecular Function (MF) ligase activity 0.1525 Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0 Highly Informative Direct
Molecular Function (MF) intramolecular transferase activity 0.000006227 Highly Informative Direct
Molecular Function (MF) kinase regulator activity 0.0000000004092 Highly Informative Direct
Molecular Function (MF) iron-sulfur cluster binding 0 Highly Informative Direct
Molecular Function (MF) sulfurtransferase activity 0.009481 Highly Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) nuclear part 1 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.02205 Informative Inherited
Cellular Component (CC) lipid droplet 0.0000006809 Highly Informative Direct
Cellular Component (CC) transcription elongation factor complex 0.00000000000007796 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)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Methyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than meth1Moderately InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups1Moderately InformativeInherited
Enzyme Commission (EC)Acting on the CH-CH group of donors0.4974Moderately InformativeInherited
Enzyme Commission (EC)With other acceptors0InformativeDirect
Enzyme Commission (EC)Sulfurtransferases0InformativeDirect
Enzyme Commission (EC)Histone acetyltransferase0.000000000002909InformativeDirect
Enzyme Commission (EC)Transferring nitrogenous groups1InformativeInherited
Enzyme Commission (EC)Other oxidoreductases0.009866Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processrRNA processing0InformativeDirect
Biological processtRNA processing0InformativeDirect
Biological processNitrogen fixation0.000006573InformativeDirect
Biological processMolybdenum cofactor biosynthesis0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPlastid1Moderately InformativeInherited
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding1Least InformativeInherited
Molecular functionIron0Moderately InformativeDirect
Molecular functionIron-sulfur0Moderately InformativeDirect
Molecular function2Fe-2S0InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Molecular functionS-adenosyl-L-methionine0InformativeDirect
Molecular functionCobalt1InformativeInherited
Molecular functionCobalamin0.0001221Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationLyase0.0000000000005625Moderately InformativeDirect
Post-translational modificationMethyltransferase0InformativeDirect
Post-translational modificationDisulfide bond0Least 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 3 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 Radical SAM enzymes 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 3 hidden Markov models representing the Radical SAM enzymes 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 ]