SUPERFAMILY 1.75 HMM library and genome assignments server

Terpenoid synthases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Terpenoid synthases [ 48575]
Superfamily:   Terpenoid synthases [ 48576] (5)
Families:   Isoprenyl diphosphate synthases [ 48577] (3)
  Squalene synthase [ 48580]
  Terpenoid cyclase C-terminal domain [ 48583] (2)
  Aristolochene/pentalenene synthase [ 48586] (2)
  Trichodiene synthase [ 69113]


Superfamily statistics
Genomes (3,137) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 16,200 51,349 30
Proteins 15,795 50,950 30


Functional annotation
General category Metabolism
Detailed category Secondary metabolism

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 process0.0000000000035180Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.000000000012070Least InformativeDirect
Biological Process (BP)multicellular organismal process0.91041Least InformativeInherited
Biological Process (BP)developmental process0.71721Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)localization0.8831Least InformativeInherited
Biological Process (BP)lipid metabolic process00Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process0.0019040.3238Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.0078040.000000000002499Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.19990.002375Moderately InformativeInherited
Biological Process (BP)organic hydroxy compound metabolic process0.0045130.006193Moderately InformativeInherited
Biological Process (BP)organ development0.26091Moderately InformativeInherited
Biological Process (BP)reproduction0.02290.9992Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.1580.00001352Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.86951Moderately InformativeInherited
Biological Process (BP)alcohol metabolic process0.00000030270.0000003478InformativeDirect
Biological Process (BP)phospholipid metabolic process0.0000043780InformativeDirect
Biological Process (BP)isoprenoid metabolic process00InformativeDirect
Biological Process (BP)cellular ketone metabolic process0.0002030.00000000000001086InformativeDirect
Biological Process (BP)organic hydroxy compound biosynthetic process0.0099150.002475InformativeInherited
Biological Process (BP)coenzyme biosynthetic process0.028160.000335InformativeInherited
Biological Process (BP)tube development0.00022240.2731InformativeInherited
Biological Process (BP)embryonic organ development0.00002780.1496InformativeInherited
Biological Process (BP)cardiovascular system development0.0011730.6019InformativeInherited
Biological Process (BP)pigment metabolic process0.0000033920.002542InformativeInherited
Biological Process (BP)cellular component movement0.0085060.8596InformativeInherited
Biological Process (BP)sexual reproduction0.0001080.1813InformativeInherited
Biological Process (BP)locomotion0.0057510.8389InformativeInherited
Biological Process (BP)single organism reproductive process0.0012310.4216InformativeInherited
Biological Process (BP)multicellular organismal reproductive process0.010470.3319InformativeInherited
Biological Process (BP)cellular process involved in reproduction0.0032990.6802InformativeInherited
Biological Process (BP)localization of cell0.0010240.2425InformativeInherited
Biological Process (BP)oxidoreduction coenzyme metabolic process0.002670.00001253InformativeInherited
Biological Process (BP)steroid biosynthetic process0.00075950.0001446Highly InformativeDirect
Biological Process (BP)isoprenoid biosynthetic process00Highly InformativeDirect
Biological Process (BP)sterol metabolic process0.000027290.000000001557Highly InformativeDirect
Biological Process (BP)quinone cofactor metabolic process0.00000064390Highly InformativeDirect
Biological Process (BP)pigment biosynthetic process0.0000019180.00006562Highly InformativeDirect
Biological Process (BP)quinone biosynthetic process0.000000000043850.00001831Highly InformativeDirect
Biological Process (BP)cellular process involved in reproduction in multicellular organism0.0034960.02769Highly InformativeInherited
Molecular Function (MF)transferase activity00.00000008548Least InformativeDirect
Molecular Function (MF)lyase activity0.015870Moderately InformativeInherited
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups00InformativeDirect
Molecular Function (MF)prenyltransferase activity0.000000030840Highly InformativeDirect
Molecular Function (MF)carbon-oxygen lyase activity, acting on phosphates00Highly InformativeDirect

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) biosynthetic process 0 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.000000000002499 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00001352 Moderately Informative Direct
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.733 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.3238 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.002375 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.006193 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.1284 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.9716 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.2562 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.9992 Moderately Informative Inherited
Biological Process (BP) alcohol metabolic process 0.0000003478 Informative Direct
Biological Process (BP) phospholipid metabolic process 0 Informative Direct
Biological Process (BP) isoprenoid metabolic process 0 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.00001253 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 0.000335 Informative Direct
Biological Process (BP) cellular ketone metabolic process 0.00000000000001086 Informative Direct
Biological Process (BP) protein oligomerization 0.08753 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.002475 Informative Inherited
Biological Process (BP) tube development 0.2731 Informative Inherited
Biological Process (BP) embryonic organ development 0.1496 Informative Inherited
Biological Process (BP) cardiovascular system development 0.6019 Informative Inherited
Biological Process (BP) pigment metabolic process 0.002542 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.004008 Informative Inherited
Biological Process (BP) lipid catabolic process 0.8211 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.9774 Informative Inherited
Biological Process (BP) cellular component movement 0.8596 Informative Inherited
Biological Process (BP) sexual reproduction 0.1813 Informative Inherited
Biological Process (BP) locomotion 0.8389 Informative Inherited
Biological Process (BP) single organism reproductive process 0.4216 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.3319 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.6802 Informative Inherited
Biological Process (BP) localization of cell 0.2425 Informative Inherited
Biological Process (BP) steroid biosynthetic process 0.0001446 Highly Informative Direct
Biological Process (BP) isoprenoid biosynthetic process 0 Highly Informative Direct
Biological Process (BP) sterol metabolic process 0.000000001557 Highly Informative Direct
Biological Process (BP) quinone cofactor metabolic process 0 Highly Informative Direct
Biological Process (BP) pigment biosynthetic process 0.00006562 Highly Informative Direct
Biological Process (BP) protein tetramerization 0.0003068 Highly Informative Direct
Biological Process (BP) quinone biosynthetic process 0.00001831 Highly Informative Direct
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.02769 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.00000008548 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) cation binding 0.0002641 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.1691 Moderately Informative Inherited
Molecular Function (MF) magnesium ion binding 0.00000000001554 Informative Direct
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.004073 Informative Inherited
Molecular Function (MF) prenyltransferase activity 0 Highly Informative Direct
Molecular Function (MF) carbon-oxygen lyase activity, acting on phosphates 0 Highly Informative Direct
Molecular Function (MF) manganese ion binding 0.000008792 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1978 Least Informative Inherited
Cellular Component (CC) plastid 0.0000000007116 Informative Direct
Cellular Component (CC) chloroplast stroma 0.000000003712 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Isomerases0.003908Least InformativeInherited
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than meth1Moderately InformativeInherited
Enzyme Commission (EC)Acting on phosphates0InformativeDirect
Enzyme Commission (EC)Intramolecular lyases1InformativeInherited

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/homeostasis0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0Moderately InformativeDirect
Phenotypic Abnormality (PA)Increased serum lactate0Highly InformativeDirect

Document: HP 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

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)cell0Least InformativeDirect

Document: FA 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)gamete0Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)megasporophyll1Least InformativeInherited
Plant ANatomical entity (PAN)microsporophyll1Least InformativeInherited
Plant ANatomical entity (PAN)flower1Least InformativeInherited
Plant ANatomical entity (PAN)collective phyllome structure1Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure1Least InformativeInherited
Plant ANatomical entity (PAN)filament0.0002034Highly InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.01648Moderately InformativeInherited
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Diphosphoric monoester hydrolases0.000000004055Highly InformativeDirect
Enzyme Commission (EC)Intramolecular lyases1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism0.00000000001098Moderately InformativeDirect
Biological processPlant defense0InformativeDirect
Biological processSteroid metabolism0InformativeDirect
Biological processLipid biosynthesis2.372e-16InformativeDirect
Biological processIsoprene biosynthesis0Highly InformativeDirect
Biological processSteroid biosynthesis0Highly InformativeDirect
Biological processSterol biosynthesis0Highly InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.000003699Moderately InformativeDirect
Cellular componentHost endoplasmic reticulum0.000004456Highly InformativeDirect
Developmental stageLate protein0.00001597Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Post-translational modificationTransferase0.0000000001635Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationIsomerase0.00008089Moderately InformativeDirect

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)cofactor metabolism1Least InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis0Moderately InformativeDirect
UniPathway (UP)lipid biosynthesis0Moderately InformativeDirect
UniPathway (UP)secondary metabolite metabolism0Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism0.7899Moderately InformativeInherited
UniPathway (UP)isoprenoid biosynthesis0InformativeDirect
UniPathway (UP)terpene metabolism0InformativeDirect
UniPathway (UP)pigment biosynthesis0InformativeDirect
UniPathway (UP)plant hormone metabolism0.000002792InformativeDirect
UniPathway (UP)alkaloid metabolism0.0002061InformativeDirect
UniPathway (UP)quinone cofactor biosynthesis0.004285InformativeInherited
UniPathway (UP)carotenoid biosynthesis0Highly InformativeDirect
UniPathway (UP)plant hormone biosynthesis0.0000002748Highly InformativeDirect
UniPathway (UP)ubiquinone biosynthesis0.00001147Highly InformativeDirect
UniPathway (UP)sesquiterpene biosynthesis0.0001834Highly InformativeDirect
UniPathway (UP)monoterpene metabolism0.3316Highly InformativeInherited

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR008949 SSF48576 Protein matches
Abstract

Terpenoid cyclases catalyze remarkably complex cyclisation cascades that are initiated by the formation of a highly reactive carbocation in a polyisoprene substrate [PubMed9914250]. The pathways of monoterpene, sesquiterpene, and diterpene biosynthesis are conveniently divided into several stages [PubMed9539701]. The first encompasses the synthesis of isopentenyl diphosphate, isomerization to dimethylallyl diphosphate, prenyltransferase-catalysed condensation of these two C5-units to geranyl diphosphate (GDP), and the subsequent 1'-4 additions of isopentenyl diphosphate to generate farnesyl (FDP) and geranylgeranyl (GGDP) diphosphate. In the second stage, the prenyl diphosphates undergo a range of cyclisations based on variations on the same mechanistic theme to produce the parent skeletons of each class. Thus, GDP (C10) gives rise to monoterpenes, FDP (C15) to sesquiterpenes, and GGDP (C20) to diterpenes. These transformations catalysed by the terpenoid synthases (cyclases) may be followed by a variety of redox modifications of the parent skeletal types to produce the many thousands of different terpenoid metabolites of the essential oils, turpentines, and resins of plant origin. Terpenoid synthases enzymes provide a template for binding and stabilizing the flexible substrate in the precise orientation required for catalysis, trigger carbocation formation, chaperone the conformations of the reactive carbocation intermediates through a unique cyclisation sequence, and sequester and stabilize carbocations from premature quenching [PubMed9914250].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · 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 11 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 Terpenoid synthases 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 11 hidden Markov models representing the Terpenoid synthases 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]