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  Home > SCOP hierarchy > ClpP/crotonase superfamily


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 (3,171) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 51,558 239,162 57
Proteins 45,650 216,986 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)biosynthetic process11Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.0041880.00000000001158Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.9021Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.97421Least InformativeInherited
Biological Process (BP)lipid metabolic process0.000000014240Moderately InformativeDirect
Biological Process (BP)monocarboxylic acid metabolic process00Moderately InformativeDirect
Biological Process (BP)cellular catabolic process0.0000000000022070Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process0.00000000053310.00000000001895Moderately InformativeDirect
Biological Process (BP)single-organism biosynthetic process0.31360.00003421Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.0048851Moderately InformativeInherited
Biological Process (BP)fatty acid metabolic process0.0000000047170InformativeDirect
Biological Process (BP)lipid catabolic process0.00000000017780InformativeDirect
Biological Process (BP)carboxylic acid catabolic process0.00000018010.0000000000001979InformativeDirect
Biological Process (BP)cellular ketone metabolic process0.069920.02052InformativeInherited
Biological Process (BP)nucleobase-containing compound catabolic process0.010520.3677InformativeInherited
Biological Process (BP)cellular macromolecule catabolic process0.000021910.02219InformativeInherited
Biological Process (BP)mRNA catabolic process0.000000026480.0001402Highly InformativeDirect
Biological Process (BP)fatty acid catabolic process0.00000049350.0000000212Highly InformativeDirect
Biological Process (BP)lipid modification0.00000000018140.00000004912Highly InformativeDirect
Biological Process (BP)quinone biosynthetic process0.00019460.000005895Highly InformativeDirect
Molecular Function (MF)hydrolase activity11Least InformativeInherited
Molecular Function (MF)lyase activity0.000000000000040050Moderately InformativeDirect
Molecular Function (MF)isomerase activity0.0000000028180.0000000006757Moderately InformativeDirect
Molecular Function (MF)hydro-lyase activity00InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity0.000070760.00000002172InformativeDirect
Molecular Function (MF)ligase activity0.019630InformativeInherited
Molecular Function (MF)carbon-carbon lyase activity0.56040.1687InformativeInherited
Molecular Function (MF)intramolecular oxidoreductase activity, transposing C=C bonds00Highly InformativeDirect
Molecular Function (MF)serine hydrolase activity0.00038420.00000004708Highly InformativeDirect
Molecular Function (MF)oxo-acid-lyase activity0.037370.1154Highly InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.00085840.000003513Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.000000000021590Least InformativeDirect
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)protein complex0.19471Least InformativeInherited
Cellular Component (CC)organelle envelope0.5920.0767Moderately InformativeInherited
Cellular Component (CC)mitochondrial part0.20790.01948Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.18471Moderately InformativeInherited
Cellular Component (CC)mitochondrial matrix0.000025470.000001156InformativeDirect
Cellular Component (CC)microbody0.0000078420InformativeDirect
Cellular Component (CC)plastid0.00380.00134InformativeInherited
Cellular Component (CC)chloroplast stroma0.000069010.03959Highly 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 0.00000000001158 Least Informative Direct
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) lipid metabolic process 0 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 biosynthetic process 0.00003421 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00001468 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.00000000001895 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.5629 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) proteolysis 0.000002071 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 0.0000000000001979 Informative Direct
Biological Process (BP) cellular ketone metabolic process 0.02052 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.04671 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 1 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.3677 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.02219 Informative Inherited
Biological Process (BP) mRNA catabolic process 0.0001402 Highly Informative Direct
Biological Process (BP) acyl-CoA metabolic process 0.00000000000394 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.0000000212 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0.0000000002978 Highly Informative Direct
Biological Process (BP) lipid modification 0.00000004912 Highly Informative Direct
Biological Process (BP) quinone biosynthetic process 0.000005895 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.0000000006757 Moderately Informative Direct
Molecular Function (MF) anion binding 0.3363 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 1 Moderately Informative Inherited
Molecular Function (MF) oxidoreductase activity 1 Moderately Informative Inherited
Molecular Function (MF) peptidase activity 0.000009535 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on CH-OH group of donors 0.00001684 Informative Direct
Molecular Function (MF) hydro-lyase activity 0 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.00000002172 Informative Direct
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) carboxylic acid binding 0.0009258 Informative Direct
Molecular Function (MF) amide binding 0.0006056 Informative Direct
Molecular Function (MF) sulfur compound binding 0.0004986 Informative Direct
Molecular Function (MF) racemase and epimerase activity 0.04712 Informative Inherited
Molecular Function (MF) carbon-carbon lyase activity 0.1687 Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 0.000004715 Highly Informative Direct
Molecular Function (MF) thiolester hydrolase activity 0.000392 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, transposing C=C bonds 0 Highly Informative Direct
Molecular Function (MF) serine hydrolase activity 0.00000004708 Highly Informative Direct
Molecular Function (MF) monocarboxylic acid binding 0.000002017 Highly Informative Direct
Molecular Function (MF) oxo-acid-lyase activity 0.1154 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.000003513 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 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) organelle envelope 0.0767 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.01948 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 0.000001156 Informative Direct
Cellular Component (CC) external encapsulating structure 0.00004548 Informative Direct
Cellular Component (CC) microbody 0 Informative Direct
Cellular Component (CC) plastid 0.00134 Informative Inherited
Cellular Component (CC) chloroplast stroma 0.03959 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

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.09928Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of carbohydrate metabolism/homeostasis0.003092Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.004167Moderately InformativeInherited
Phenotypic Abnormality (PA)Hyperammonemia0.00005692InformativeDirect
Phenotypic Abnormality (PA)Hypoglycemia0.0001018InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0.08254Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.0002745Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal hormone level0.08276Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal fatty acid level0.0000001507Highly InformativeDirect
Mammalian Phenotype (MP)increased circulating insulin level0.0003126Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)pigmentation variant0.004483InformativeInherited
Worm Phenotype (WP)clear0.0003631Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)heart0.0009532InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
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)portion of meristem tissue0.00006271Least InformativeDirect
Plant ANatomical entity (PAN)seed0.0002568Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.0004483Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0.004092Least InformativeInherited
Plant ANatomical entity (PAN)inflorescence0.01686Least InformativeInherited
Plant ANatomical entity (PAN)megasporophyll0.04441Least InformativeInherited
Plant ANatomical entity (PAN)leaf0.1769Least InformativeInherited
Plant ANatomical entity (PAN)microsporophyll0.8755Least InformativeInherited
Plant structure DEvelopment stage (PDE)F mature embryo stage0.0001658Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Lyases0.0000000002105Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Acting on the CH-OH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.000000000002901Moderately InformativeDirect
Enzyme Commission (EC)Carbon-carbon lyases1Moderately InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0InformativeDirect
Enzyme Commission (EC)Racemases and epimerases0InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0.000000000000008035InformativeDirect
Enzyme Commission (EC)Carboxy-lyases1InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases1InformativeInherited
Enzyme Commission (EC)Transposing C==C bonds0Highly InformativeDirect
Enzyme Commission (EC)Biotin carboxylase0Highly InformativeDirect
Enzyme Commission (EC)Oxo-acid-lyases0.0004654Highly InformativeDirect
Enzyme Commission (EC)Ligases that form carbon-carbon bonds1Highly InformativeInherited

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)alimentary tract and metabolism0Least InformativeDirect
Drugbank ATC_code (DB)other plain vitamin preparations1Moderately InformativeInherited
Drugbank ATC_code (DB)biotin0.00000000005464InformativeDirect

Document: DB 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 biosynthesis0.000117InformativeDirect
Biological processMenaquinone biosynthesis0.0000006939Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentPeroxisome0.0000000006415InformativeDirect
Coding sequence diversityRNA editing0.0000006087Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainTransit peptide0.000000000000008402Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionBiotin0Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationSerine protease0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)lipid metabolism0Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)aromatic compound metabolism1Least InformativeInherited
UniPathway (UP)fatty acid metabolism0Moderately InformativeDirect
UniPathway (UP)metabolic intermediate biosynthesis0Moderately InformativeDirect
UniPathway (UP)lipid biosynthesis0.001351Moderately InformativeInherited
UniPathway (UP)aromatic compound degradation0.07206Moderately InformativeInherited
UniPathway (UP)amino-acid degradation0.6408Moderately InformativeInherited
UniPathway (UP)amine and polyamine metabolism1Moderately InformativeInherited
UniPathway (UP)fatty acid biosynthesis0InformativeDirect
UniPathway (UP)Branched-chain amino-acid degradation0InformativeDirect
UniPathway (UP)carnitine metabolism0.000000002353InformativeDirect
UniPathway (UP)fatty acid degradation0.0002658InformativeDirect
UniPathway (UP)metabolic intermediate degradation0.0005799InformativeDirect
UniPathway (UP)xenobiotic degradation1InformativeInherited
UniPathway (UP)malonyl-CoA biosynthesis0Highly InformativeDirect
UniPathway (UP)propanoyl-CoA degradation0Highly 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) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · 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 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) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

Please send feedback, comments or questions to superfamily@cs.bris.ac.uk or use the feedback form.

© Copyright 2013 The SUPERFAMILY authors and Julian Gough.