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ClpP/crotonase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   ClpP/crotonase [ 52095]
Superfamily:   ClpP/crotonase [ 52096] (4)
Families:   Clp protease, ClpP subunit [ 52097]
  Tail specific protease, catalytic domain [ 52100] (3)
  Crotonase-like [ 52103] (13)
  Biotin dependent carboxylase carboxyltransferase domain [ 89572] (6)


Superfamily statistics
Genomes (3,178) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 51,793 326,316 57
Proteins 45,853 288,287 47


Functional annotation
General category Processes_IC
Detailed category Proteases

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 process0.00006140Least InformativeDirect
Biological Process (BP)primary metabolic process0.46030.6025Least InformativeInherited
Biological Process (BP)biosynthetic process11Least InformativeInherited
Biological Process (BP)single-organism cellular process0.031740.0124Least InformativeInherited
Biological Process (BP)macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)lipid metabolic process0.000000022580Moderately InformativeDirect
Biological Process (BP)monocarboxylic acid metabolic process0.0000000061190Moderately InformativeDirect
Biological Process (BP)cellular catabolic process0.000000000043790Moderately InformativeDirect
Biological Process (BP)single-organism catabolic process0.0000028840Moderately InformativeDirect
Biological Process (BP)oxidation-reduction process0.00050130.000004234Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process0.000000020290Moderately InformativeDirect
Biological Process (BP)small molecule biosynthetic process0.40990.02301Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.27390.00000001719Moderately InformativeInherited
Biological Process (BP)proteolysis0.000024950.0000002044InformativeDirect
Biological Process (BP)fatty acid metabolic process0.000000000035560InformativeDirect
Biological Process (BP)lipid catabolic process0.0000000000034030InformativeDirect
Biological Process (BP)carboxylic acid catabolic process0.000000001070InformativeDirect
Biological Process (BP)coenzyme biosynthetic process0.049650.5039InformativeInherited
Biological Process (BP)cellular ketone metabolic process0.0046160.004721InformativeInherited
Biological Process (BP)fatty acid catabolic process0.0000000015880.00000000000002769Highly InformativeDirect
Biological Process (BP)lipid modification0.000000025570.000000719Highly InformativeDirect
Biological Process (BP)ketone biosynthetic process0.0000067880.00003845Highly InformativeDirect
Biological Process (BP)quinone metabolic process0.000006840.009657Highly InformativeInherited
Molecular Function (MF)hydrolase activity11Least InformativeInherited
Molecular Function (MF)lyase activity0.000000000000011250Moderately InformativeDirect
Molecular Function (MF)isomerase activity0.00000031230.000000000001221Moderately InformativeDirect
Molecular Function (MF)hydro-lyase activity00InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity0.00035380.000000783InformativeDirect
Molecular Function (MF)ligase activity0.05590InformativeInherited
Molecular Function (MF)carbon-carbon lyase activity0.55970.5481InformativeInherited
Molecular Function (MF)intramolecular oxidoreductase activity, transposing C=C bonds00Highly InformativeDirect
Molecular Function (MF)serine hydrolase activity0.000023360.0000000001796Highly InformativeDirect
Molecular Function (MF)oxo-acid-lyase activity0.017920.05083Highly InformativeInherited
Cellular Component (CC)cytoplasmic part0.0000042490.000000000009676Least InformativeDirect
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)protein complex0.46631Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.00058460.005706Least InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.53971Moderately InformativeInherited
Cellular Component (CC)microbody0.000000019560InformativeDirect
Cellular Component (CC)plastid0.0014250.00004958InformativeInherited
Cellular Component (CC)thylakoid0.00096970.000000009601Highly InformativeDirect
Cellular Component (CC)chloroplast stroma0.00014430.019Highly 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) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.6025 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.0124 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.00001451 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00000001719 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.000004234 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.02301 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.1445 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) proteolysis 0.0000002044 Informative Direct
Biological Process (BP) fatty acid metabolic process 0 Informative Direct
Biological Process (BP) lipid catabolic process 0 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0.2283 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0.5039 Informative Inherited
Biological Process (BP) cellular ketone metabolic process 0.004721 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.01836 Informative Inherited
Biological Process (BP) fatty acid catabolic process 0.00000000000002769 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0.000000000004596 Highly Informative Direct
Biological Process (BP) lipid modification 0.000000719 Highly Informative Direct
Biological Process (BP) ketone biosynthetic process 0.00003845 Highly Informative Direct
Biological Process (BP) quinone metabolic process 0.009657 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.000000000001221 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.003067 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.004984 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 1 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.1437 Moderately Informative Inherited
Molecular Function (MF) oxidoreductase activity 1 Moderately Informative Inherited
Molecular Function (MF) hydro-lyase activity 0 Informative Direct
Molecular Function (MF) racemase and epimerase activity 0.0005065 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.000000783 Informative Direct
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) carboxylic acid binding 0.000000001116 Informative Direct
Molecular Function (MF) amide binding 0.00003493 Informative Direct
Molecular Function (MF) sulfur compound binding 0.0000001438 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.02988 Informative Inherited
Molecular Function (MF) ribonucleotide binding 0.02148 Informative Inherited
Molecular Function (MF) carbon-carbon lyase activity 0.5481 Informative Inherited
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 1 Informative Inherited
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.103 Informative Inherited
Molecular Function (MF) ATP binding 0.0004278 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 0.00000000001331 Highly Informative Direct
Molecular Function (MF) thiolester hydrolase activity 0.000004421 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, transposing C=C bonds 0 Highly Informative Direct
Molecular Function (MF) serine hydrolase activity 0.0000000001796 Highly Informative Direct
Molecular Function (MF) isoprenoid binding 0.0000000006 Highly Informative Direct
Molecular Function (MF) vitamin binding 8.27e-16 Highly Informative Direct
Molecular Function (MF) monocarboxylic acid binding 0.000000000000001615 Highly Informative Direct
Molecular Function (MF) alcohol binding 0.000003378 Highly Informative Direct
Molecular Function (MF) oxo-acid-lyase activity 0.05083 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.000000000009676 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.005706 Least Informative Inherited
Cellular Component (CC) extracellular region part 0.6421 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) plastid 0.00004958 Informative Direct
Cellular Component (CC) external encapsulating structure 0.0003151 Informative Direct
Cellular Component (CC) microbody 0 Informative Direct
Cellular Component (CC) thylakoid 0.000000009601 Highly Informative Direct
Cellular Component (CC) chloroplast stroma 0.019 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Isomerases0.000000000008328Least InformativeDirect
Enzyme Commission (EC)Lyases0.000000003872Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds1Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Serine endopeptidases0Moderately InformativeDirect
Enzyme Commission (EC)Racemases and epimerases0Moderately InformativeDirect
Enzyme Commission (EC)Hydro-lyases0Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0.00000000000001918Moderately InformativeDirect
Enzyme Commission (EC)Forming carbon-nitrogen bonds1Moderately InformativeInherited
Enzyme Commission (EC)Carboxy-lyases1Moderately InformativeInherited
Enzyme Commission (EC)Transposing C==C bonds0InformativeDirect
Enzyme Commission (EC)Thiolester hydrolases0.00001714InformativeDirect
Enzyme Commission (EC)Oxo-acid-lyases0.00008764InformativeDirect
Enzyme Commission (EC)Ligases that form carbon-carbon bonds1InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases1InformativeInherited
Enzyme Commission (EC)3-hydroxybutyryl-CoA epimerase0Highly InformativeDirect
Enzyme Commission (EC)Biotin carboxylase0Highly InformativeDirect
Enzyme Commission (EC)3-hydroxyacyl-CoA dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)Dodecenoyl-CoA isomerase0Highly InformativeDirect
Enzyme Commission (EC)Enoyl-CoA hydratase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism0Moderately InformativeDirect
Biological processFatty acid metabolism0InformativeDirect
Biological processLipid biosynthesis0.000008032InformativeDirect
Biological processMenaquinone biosynthesis0.000000345Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentPeroxisome0.0000000000003644InformativeDirect
Coding sequence diversityRNA editing0.0000006065Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainTransit peptide0.00000000000000185Moderately InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionBiotin0Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationSerine protease0InformativeDirect

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 38 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 ClpP/crotonase 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 38 hidden Markov models representing the ClpP/crotonase 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 ]