SUPERFAMILY 1.75 HMM library and genome assignments server


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 (3,183) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8,907 69,010 15
Proteins 8,770 68,675 15


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) nitrogen compound metabolic process 8.449e-12 Least Informative Direct
Biological Process (BP) single-organism metabolic process 1.376e-12 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 2.046e-12 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 4.171e-11 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 7.662e-11 Least Informative Direct
Biological Process (BP) biosynthetic process 1.202e-10 Least Informative Direct
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) organophosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0 Informative Direct
Biological Process (BP) deoxyribonucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) deoxyribose phosphate metabolic process 3.424e-14 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) nucleotide binding 0.0003671 Informative Direct
Cellular Component (CC) protein complex 0.0324 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.424 Least Informative Inherited

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 groups7.321e-06Moderately 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

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Acyltransferases9.699e-05Moderately InformativeDirect
Enzyme Commission (EC)Carbon-carbon lyases0.2246Moderately InformativeInherited
Enzyme Commission (EC)Acting on CH or CH(2) groups0InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0.1813InformativeInherited
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 metabolism0.0005145Moderately InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processDNA synthesis0Highly InformativeDirect
Biological processGlucose metabolism6.643e-15Highly InformativeDirect
Developmental stageEarly protein0.0008503Least InformativeDirect
DomainRedox-active center9.582e-15InformativeDirect
Molecular functionNucleotide-binding2.224e-14Least InformativeDirect
Molecular functionCobalt0InformativeDirect
Molecular functionCobalamin0Highly InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationAcyltransferase1.123e-06InformativeDirect
Post-translational modificationDisulfide bond1.506e-10Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)carbohydrate metabolism0.4448Least InformativeInherited
UniPathway (UP)organic acid metabolism4.118e-12Moderately InformativeDirect
UniPathway (UP)fermentation2.274e-16InformativeDirect
UniPathway (UP)metabolic intermediate degradation1.788e-15InformativeDirect
UniPathway (UP)organic acid degradation6.099e-14InformativeDirect
UniPathway (UP)pyruvate metabolism0Highly InformativeDirect
UniPathway (UP)DNA replication0Highly InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · 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 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-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]