SUPERFAMILY 1.75 HMM library and genome assignments server

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PFL-like glycyl radical enzymes superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   PFL-like glycyl radical enzymes [ 51997]
Superfamily:   PFL-like glycyl radical enzymes [ 51998] (5)
Families:   PFL-like [ 51999] (2)
  R1 subunit of ribonucleotide reductase, C-terminal domain [ 52002]
  B12-dependent (class II) ribonucleotide reductase [ 75131]
  Class III anaerobic ribonucleotide reductase NRDD subunit [ 52005]
  SP0239-like [ 159444]


Superfamily statistics
Genomes (3,198) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 8,918 54,863 15
Proteins 8,781 54,309 15


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)single-organism metabolic process0.0023370Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.025420.000000000006246Least InformativeInherited
Biological Process (BP)biosynthetic process0.12710.0000000001696Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.097240.0000000004559Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.098530.0000000003095Least InformativeInherited
Biological Process (BP)single-organism cellular process0.028150.0000003173Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.1380.0000000003839Least InformativeInherited
Biological Process (BP)primary metabolic process0.56440.13Least InformativeInherited
Biological Process (BP)nucleoside phosphate metabolic process0.000040160Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.00043880Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.00022470Moderately InformativeDirect
Biological Process (BP)organophosphate biosynthetic process0.000016010Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process0.00066080Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.00071610Moderately InformativeDirect
Biological Process (BP)nucleotide biosynthetic process0.00000044240.000000000003094InformativeDirect
Biological Process (BP)deoxyribonucleotide metabolic process0.0000000015920Highly InformativeDirect
Biological Process (BP)deoxyribose phosphate metabolic process0.00000000091650.0000000000005848Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity0.001420Moderately InformativeInherited

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 0.0000000004559 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0000000001696 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0000000003839 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0000003173 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0000000003095 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000000006246 Least Informative Direct
Biological Process (BP) primary metabolic process 0.13 Least Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.000000000003094 Informative Direct
Biological Process (BP) deoxyribonucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) deoxyribose phosphate metabolic process 0.0000000000005848 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Cellular Component (CC) cytoplasmic part 0.1906 Least Informative Inherited
Cellular Component (CC) cytosolic part 0.000000000006557 Moderately Informative Direct
Cellular Component (CC) oxidoreductase complex 0.000000000000005967 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0.000007321Moderately InformativeDirect
Enzyme Commission (EC)Acting on CH or CH(2) groups0InformativeDirect
Enzyme Commission (EC)With a disulfide as acceptor0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCarbohydrate metabolism0.0007532Moderately InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processDNA synthesis0Highly InformativeDirect
Biological processGlucose metabolism0.00000000000001819Highly InformativeDirect
Cellular componentHost cytoplasm0.000006438InformativeDirect
DomainRedox-active center0.00000000000002259InformativeDirect
Molecular functionNucleotide-binding0.000000000000003433Least InformativeDirect
Molecular functionCobalt0InformativeDirect
Molecular functionCobalamin0Highly InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationAcyltransferase0.000002132InformativeDirect
Post-translational modificationDisulfide bond0.000000000003571Least 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 7 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 PFL-like glycyl radical 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 7 hidden Markov models representing the PFL-like glycyl radical 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 ]