SUPERFAMILY 1.75 HMM library and genome assignments server

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 (3,177) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 45,926 251,108 3
Proteins 45,656 250,428 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)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process00Least InformativeDirect
Biological Process (BP)biosynthetic process00.000000000000007248Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.000000000049570.0000000002857Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.0084110.1632Least InformativeInherited
Biological Process (BP)single-organism cellular process0.38691Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.0017860.01291Least InformativeInherited
Biological Process (BP)protein metabolic process0.43180.1961Least InformativeInherited
Biological Process (BP)regulation of cellular process11Least InformativeInherited
Biological Process (BP)developmental process11Least InformativeInherited
Biological Process (BP)multicellular organismal process11Least InformativeInherited
Biological Process (BP)response to stimulus11Least InformativeInherited
Biological Process (BP)positive regulation of biological process0.96291Least InformativeInherited
Biological Process (BP)heterocycle biosynthetic process00Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process00Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process00Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.000000000000047780Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process0.0000000000028470.000000526Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.000000021430.0001304Moderately InformativeDirect
Biological Process (BP)sulfur compound metabolic process0.0000260.0000005489Moderately InformativeDirect
Biological Process (BP)positive regulation of response to stimulus0.10681Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process0.68361Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process0.083070.1036Moderately InformativeInherited
Biological Process (BP)response to external stimulus0.13591Moderately InformativeInherited
Biological Process (BP)defense response0.049710.2621Moderately InformativeInherited
Biological Process (BP)regulation of localization0.1390.527Moderately InformativeInherited
Biological Process (BP)organ development0.31031Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.4940.06154Moderately InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.92780.8115Moderately InformativeInherited
Biological Process (BP)immune system process0.32071Moderately InformativeInherited
Biological Process (BP)cell differentiation0.41861Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process0.75851Moderately InformativeInherited
Biological Process (BP)regulation of signal transduction0.14911Moderately InformativeInherited
Biological Process (BP)multi-organism process0.43221Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.0049970.0001006Moderately InformativeInherited
Biological Process (BP)lipid metabolic process0.77930.423Moderately InformativeInherited
Biological Process (BP)regulation of multicellular organismal process0.085111Moderately InformativeInherited
Biological Process (BP)tetrapyrrole metabolic process00InformativeDirect
Biological Process (BP)pigment metabolic process0.00000000000052150.0000000000000567InformativeDirect
Biological Process (BP)monocarboxylic acid biosynthetic process0.000089740.000001467InformativeDirect
Biological Process (BP)vitamin metabolic process0.00012220.000001271InformativeDirect
Biological Process (BP)regulation of immune response0.0078960.278InformativeInherited
Biological Process (BP)regulation of cytokine production0.000068470.02146InformativeInherited
Biological Process (BP)immune effector process0.0006380.0338InformativeInherited
Biological Process (BP)defense response to other organism0.0076790.133InformativeInherited
Biological Process (BP)negative regulation of transport0.000044460.006029InformativeInherited
Biological Process (BP)regulation of protein localization0.00047140.04946InformativeInherited
Biological Process (BP)regulation of secretion0.00046370.05866InformativeInherited
Biological Process (BP)leukocyte activation0.000046820.02856InformativeInherited
Biological Process (BP)hematopoietic or lymphoid organ development0.00018420.1509InformativeInherited
Biological Process (BP)fatty acid metabolic process0.030440.001144InformativeInherited
Biological Process (BP)sulfur compound biosynthetic process0.001690.00001245InformativeInherited
Biological Process (BP)coenzyme biosynthetic process10.986InformativeInherited
Biological Process (BP)positive regulation of multicellular organismal process0.0071170.7574InformativeInherited
Biological Process (BP)regulation of immune effector process0.00001020.005939InformativeInherited
Biological Process (BP)positive regulation of immune system process0.0036380.1657InformativeInherited
Biological Process (BP)heme metabolic process00Highly InformativeDirect
Biological Process (BP)regulation of toll-like receptor signaling pathway0.0000000000036760.000000006055Highly InformativeDirect
Biological Process (BP)alpha-beta T cell activation0.00000000071390.0000006964Highly InformativeDirect
Biological Process (BP)porphyrin-containing compound biosynthetic process0.0000000015620.00003589Highly InformativeDirect
Biological Process (BP)pigment biosynthetic process0.0000000015870.00000000008808Highly InformativeDirect
Biological Process (BP)regulation of cytokine production involved in immune response0.0000000024650.00000004783Highly InformativeDirect
Biological Process (BP)positive regulation of production of molecular mediator of immune response0.000000006150.000000616Highly InformativeDirect
Biological Process (BP)positive regulation of lymphocyte mediated immunity0.000000025130.000006657Highly InformativeDirect
Biological Process (BP)regulation of adaptive immune response0.000000027620.00003967Highly InformativeDirect
Biological Process (BP)T cell differentiation0.000000056580.0002138Highly InformativeDirect
Biological Process (BP)negative regulation of secretion by cell0.00000013390.00003739Highly InformativeDirect
Biological Process (BP)negative regulation of protein transport0.00000021840.0000433Highly InformativeDirect
Biological Process (BP)response to virus0.0000019680.0003158Highly InformativeDirect
Biological Process (BP)molybdopterin cofactor metabolic process0.000010780Highly InformativeDirect
Biological Process (BP)positive regulation of cytokine production0.0000082820.002485Highly InformativeInherited
Molecular Function (MF)binding0.040261Least InformativeInherited
Molecular Function (MF)transferase activity0.60370.2405Least InformativeInherited
Molecular Function (MF)oxidoreductase activity0.000012840.0002744Moderately InformativeDirect
Molecular Function (MF)lyase activity0.055370.007734Moderately InformativeInherited
Molecular Function (MF)transferase activity, transferring sulfur-containing groups0.0000000000034480InformativeDirect
Molecular Function (MF)carbon-carbon lyase activity0.0039060.00005793InformativeInherited
Molecular Function (MF)ligase activity0.0068580.0006982InformativeInherited
Molecular Function (MF)metal cluster binding00Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the CH-CH group of donors0.000000000000042820.000000000000001593Highly InformativeDirect
Molecular Function (MF)sulfurtransferase activity0.00017170.0005745Highly InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle0.81421Least InformativeInherited
Cellular Component (CC)lipid particle0.0000017740.00009694InformativeDirect

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) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0.000000000000007248 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0000000002857 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.1632 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.01291 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.1961 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 1 Least Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.000000526 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0001304 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.0000005489 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.0001006 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.1036 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) defense response 0.2621 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.2111 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.527 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) immune system process 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) gene expression 0.3404 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.06154 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.8115 Moderately Informative Inherited
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.3475 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.423 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.3379 Moderately Informative Inherited
Biological Process (BP) regulation of phosphorus metabolic process 0.2302 Moderately Informative Inherited
Biological Process (BP) tetrapyrrole metabolic process 0 Informative Direct
Biological Process (BP) pigment metabolic process 0.0000000000000567 Informative Direct
Biological Process (BP) monocarboxylic acid biosynthetic process 0.000001467 Informative Direct
Biological Process (BP) vitamin metabolic process 0.000001271 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0.00001245 Informative Direct
Biological Process (BP) RNA modification 0.000001947 Informative Direct
Biological Process (BP) regulation of transferase activity 0.0002042 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.0003219 Informative Direct
Biological Process (BP) regulation of immune response 0.278 Informative Inherited
Biological Process (BP) regulation of cytokine production 0.02146 Informative Inherited
Biological Process (BP) immune effector process 0.0338 Informative Inherited
Biological Process (BP) defense response to other organism 0.133 Informative Inherited
Biological Process (BP) negative regulation of transport 0.006029 Informative Inherited
Biological Process (BP) regulation of protein localization 0.04946 Informative Inherited
Biological Process (BP) regulation of secretion 0.05866 Informative Inherited
Biological Process (BP) leukocyte activation 0.02856 Informative Inherited
Biological Process (BP) hematopoietic or lymphoid organ development 0.1509 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.08121 Informative Inherited
Biological Process (BP) amide biosynthetic process 0.1189 Informative Inherited
Biological Process (BP) RNA processing 0.00739 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0.986 Informative Inherited
Biological Process (BP) fatty acid metabolic process 0.001144 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.7574 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.005939 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.1657 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.001482 Informative Inherited
Biological Process (BP) heme metabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of toll-like receptor signaling pathway 0.000000006055 Highly Informative Direct
Biological Process (BP) alpha-beta T cell activation 0.0000006964 Highly Informative Direct
Biological Process (BP) porphyrin-containing compound biosynthetic process 0.00003589 Highly Informative Direct
Biological Process (BP) pigment biosynthetic process 0.00000000008808 Highly Informative Direct
Biological Process (BP) regulation of cytokine production involved in immune response 0.00000004783 Highly Informative Direct
Biological Process (BP) positive regulation of production of molecular mediator of immune response 0.000000616 Highly Informative Direct
Biological Process (BP) positive regulation of lymphocyte mediated immunity 0.000006657 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response 0.00003967 Highly Informative Direct
Biological Process (BP) T cell differentiation 0.0002138 Highly Informative Direct
Biological Process (BP) negative regulation of secretion by cell 0.00003739 Highly Informative Direct
Biological Process (BP) negative regulation of protein transport 0.0000433 Highly Informative Direct
Biological Process (BP) response to virus 0.0003158 Highly Informative Direct
Biological Process (BP) molybdopterin cofactor metabolic process 0 Highly Informative Direct
Biological Process (BP) tRNA modification 0.000000001167 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.006921 Highly Informative Inherited
Biological Process (BP) positive regulation of cytokine production 0.002485 Highly Informative Inherited
Biological Process (BP) regulation of protein serine/threonine kinase activity 0.9407 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 0.2405 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0.0002744 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.007734 Moderately Informative Inherited
Molecular Function (MF) enzyme regulator activity 0.001257 Moderately Informative Inherited
Molecular Function (MF) isomerase activity 0.01397 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring sulfur-containing groups 0 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.00005793 Informative Direct
Molecular Function (MF) ligase activity 0.0006982 Informative Direct
Molecular Function (MF) metal cluster binding 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.000000000000001593 Highly Informative Direct
Molecular Function (MF) sulfurtransferase activity 0.0005745 Highly Informative Direct
Molecular Function (MF) protein kinase regulator activity 0.00000000004249 Highly Informative Direct
Molecular Function (MF) intramolecular transferase activity 0.000002363 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.3859 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.6769 Moderately Informative Inherited
Cellular Component (CC) lipid particle 0.00009694 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0007113 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

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0Least InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)lung0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0.04647Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.0000001397Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Histone acetyltransferase0.000000001005InformativeDirect
Enzyme Commission (EC)Carbon-nitrogen lyases0.006851InformativeInherited
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Intramolecular transferases (mutases)1InformativeInherited
Enzyme Commission (EC)Other carbon-carbon lyases0Highly InformativeDirect
Enzyme Commission (EC)Transferring nitrogenous groups1Highly InformativeInherited
Enzyme Commission (EC)Sulfurtransferases1Highly InformativeInherited
Enzyme Commission (EC)Oxo-acid-lyases1Highly 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 fixation0.00009858InformativeDirect
Biological processMolybdenum cofactor biosynthesis0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPlastid1Moderately InformativeInherited
Cellular componentLipid droplet0.0001859Highly InformativeDirect
DomainTransit peptide0.00000000001127Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding1Least InformativeInherited
Molecular functionIron0Moderately InformativeDirect
Molecular function2Fe-2S0InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionGTP-binding0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Molecular functionS-adenosyl-L-methionine0InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationLyase0.000000007103Moderately InformativeDirect
Post-translational modificationMethyltransferase0.00000000000001562InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)cofactor metabolism0Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)aromatic compound metabolism1Least InformativeInherited
UniPathway (UP)amino-acid degradation1Moderately InformativeInherited
UniPathway (UP)purine metabolism1Moderately InformativeInherited
UniPathway (UP)protein maturation0InformativeDirect
UniPathway (UP)purine base metabolism0.0000000000005905InformativeDirect
UniPathway (UP)tRNA modification1InformativeInherited
UniPathway (UP)quinone cofactor biosynthesis1InformativeInherited
UniPathway (UP)biotin biosynthesis0Highly InformativeDirect
UniPathway (UP)molybdopterin biosynthesis0Highly InformativeDirect
UniPathway (UP)protein lipoylation0Highly InformativeDirect
UniPathway (UP)pyrroloquinoline quinone biosynthesis0Highly InformativeDirect
UniPathway (UP)purine base biosynthesis0.000000000000008821Highly InformativeDirect
UniPathway (UP)tRNA post-transcriptional modification0.0000000006098Highly InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]