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 (2,419) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 12,645 25,224 30
Proteins 12,390 24,944 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 process1.158e-070Least InformativeDirect
Biological Process (BP)single-organism metabolic process1.248e-070Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)multicellular organismal process0.54071Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)localization0.5411Least InformativeInherited
Biological Process (BP)lipid biosynthetic process1.452e-090Moderately InformativeDirect
Biological Process (BP)cellular lipid metabolic process00Moderately InformativeDirect
Biological Process (BP)small molecule biosynthetic process8.715e-090Moderately InformativeDirect
Biological Process (BP)organic hydroxy compound metabolic process0.0011440.001239Moderately InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.0012770.2662Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.0273.618e-13Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.12331.025e-05Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.25030.794Moderately InformativeInherited
Biological Process (BP)reproduction0.0081740.9513Moderately InformativeInherited
Biological Process (BP)alcohol metabolic process3.888e-064.798e-07InformativeDirect
Biological Process (BP)phospholipid metabolic process0.0003380InformativeDirect
Biological Process (BP)isoprenoid metabolic process00InformativeDirect
Biological Process (BP)steroid metabolic process0.00025966.787e-05InformativeDirect
Biological Process (BP)cellular ketone metabolic process6.457e-052.615e-14InformativeDirect
Biological Process (BP)organic hydroxy compound biosynthetic process0.00019220.0004879InformativeDirect
Biological Process (BP)coenzyme biosynthetic process0.052740.0006167InformativeInherited
Biological Process (BP)cellular component movement0.0039750.4096InformativeInherited
Biological Process (BP)sexual reproduction4.062e-050.08337InformativeInherited
Biological Process (BP)locomotion0.0044960.7389InformativeInherited
Biological Process (BP)single organism reproductive process0.00058370.2475InformativeInherited
Biological Process (BP)multicellular organismal reproductive process0.015240.1971InformativeInherited
Biological Process (BP)cellular process involved in reproduction0.0044620.6949InformativeInherited
Biological Process (BP)localization of cell0.00086070.1727InformativeInherited
Biological Process (BP)steroid biosynthetic process3.632e-053.426e-05Highly InformativeDirect
Biological Process (BP)isoprenoid biosynthetic process00Highly InformativeDirect
Biological Process (BP)germ cell migration1.928e-063.416e-09Highly InformativeDirect
Biological Process (BP)sterol metabolic process1.961e-052.146e-09Highly InformativeDirect
Biological Process (BP)quinone cofactor metabolic process1.156e-050Highly InformativeDirect
Biological Process (BP)alcohol biosynthetic process8.636e-066.028e-06Highly InformativeDirect
Biological Process (BP)quinone biosynthetic process2.022e-126.758e-07Highly InformativeDirect
Molecular Function (MF)transferase activity1.143e-135.418e-06Least InformativeDirect
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)lyase activity0.0029070Moderately InformativeInherited
Molecular Function (MF)cation binding0.075088.369e-06Moderately InformativeInherited
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups00InformativeDirect
Molecular Function (MF)carbon-oxygen lyase activity2.643e-100InformativeDirect
Molecular Function (MF)magnesium ion binding0.00032664.008e-12Highly InformativeDirect
Molecular Function (MF)prenyltransferase activity4.244e-070Highly 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) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 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 biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 3.618e-13 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 1.025e-05 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 0.001239 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.9071 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.3556 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.6721 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.2662 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.794 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.0159 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.4701 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.04181 Moderately Informative Inherited
Biological Process (BP) reproduction 0.9513 Moderately Informative Inherited
Biological Process (BP) alcohol metabolic process 4.798e-07 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 3.093e-05 Informative Direct
Biological Process (BP) steroid metabolic process 6.787e-05 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 0.0006167 Informative Direct
Biological Process (BP) response to hormone stimulus 0.0003293 Informative Direct
Biological Process (BP) cellular ketone metabolic process 2.615e-14 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 0.0004879 Informative Direct
Biological Process (BP) response to other organism 0.3694 Informative Inherited
Biological Process (BP) protein oligomerization 0.1406 Informative Inherited
Biological Process (BP) cellular component movement 0.4096 Informative Inherited
Biological Process (BP) sexual reproduction 0.08337 Informative Inherited
Biological Process (BP) locomotion 0.7389 Informative Inherited
Biological Process (BP) single organism reproductive process 0.2475 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.1971 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.6949 Informative Inherited
Biological Process (BP) localization of cell 0.1727 Informative Inherited
Biological Process (BP) steroid biosynthetic process 3.426e-05 Highly Informative Direct
Biological Process (BP) isoprenoid biosynthetic process 0 Highly Informative Direct
Biological Process (BP) germ cell migration 3.416e-09 Highly Informative Direct
Biological Process (BP) sterol metabolic process 2.146e-09 Highly Informative Direct
Biological Process (BP) quinone cofactor metabolic process 0 Highly Informative Direct
Biological Process (BP) alcohol biosynthetic process 6.028e-06 Highly Informative Direct
Biological Process (BP) protein tetramerization 0.0001055 Highly Informative Direct
Biological Process (BP) quinone biosynthetic process 6.758e-07 Highly Informative Direct
Molecular Function (MF) transferase activity 5.418e-06 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 8.369e-06 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.1673 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0 Informative Direct
Molecular Function (MF) carbon-oxygen lyase activity 0 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.002428 Informative Inherited
Molecular Function (MF) transition metal ion binding 1 Informative Inherited
Molecular Function (MF) magnesium ion binding 4.008e-12 Highly Informative Direct
Molecular Function (MF) prenyltransferase activity 0 Highly Informative Direct
Molecular Function (MF) carbon-oxygen lyase activity, acting on phosphates 0 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.003233 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.5174 Least Informative Inherited
Cellular Component (CC) plastid 3.629e-10 Informative Direct
Cellular Component (CC) chloroplast stroma 5.668e-10 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

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)lethal0Least InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect
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)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)androecium1Least InformativeInherited
Plant ANatomical entity (PAN)gynoecium1Least InformativeInherited
Plant ANatomical entity (PAN)stalk1Least InformativeInherited
Plant ANatomical entity (PAN)filament0.0002812Highly 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)Isomerases0.04685Moderately InformativeInherited
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Diphosphoric monoester hydrolases4.447e-09Highly 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 metabolism4.472e-12Moderately InformativeDirect
Biological processLipid biosynthesis0InformativeDirect
Biological processPlant defense0InformativeDirect
Biological processSteroid metabolism0InformativeDirect
Biological processCholesterol biosynthesis0Highly InformativeDirect
Biological processIsoprene biosynthesis0Highly InformativeDirect
Biological processSteroid biosynthesis0Highly InformativeDirect
Biological processSterol biosynthesis0Highly InformativeDirect
Biological processUbiquinone biosynthesis4.993e-07Highly InformativeDirect
Biological processChlorophyll biosynthesis5.358e-05Highly InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentEndoplasmic reticulum1.457e-06Moderately InformativeDirect
Cellular componentHost endoplasmic reticulum4.403e-06Highly InformativeDirect
Developmental stageLate protein1.362e-05Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Post-translational modificationTransferase3.138e-10Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationIsomerase0.000409Moderately 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 metabolism0.7539Moderately InformativeInherited
UniPathway (UP)isoprenoid biosynthesis0InformativeDirect
UniPathway (UP)terpene metabolism0InformativeDirect
UniPathway (UP)pigment biosynthesis0InformativeDirect
UniPathway (UP)hormone metabolism1.106e-05InformativeDirect
UniPathway (UP)alkaloid metabolism8.553e-05InformativeDirect
UniPathway (UP)quinone cofactor biosynthesis0.00322InformativeInherited
UniPathway (UP)carotenoid biosynthesis0Highly InformativeDirect
UniPathway (UP)plant hormone biosynthesis9.82e-08Highly InformativeDirect
UniPathway (UP)ubiquinone biosynthesis8.863e-06Highly InformativeDirect
UniPathway (UP)sesquiterpene biosynthesis2.692e-05Highly InformativeDirect

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) · 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) · 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 ]