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Thiamin diphosphate-binding fold (THDP-binding) superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Thiamin diphosphate-binding fold (THDP-binding) [ 52517]
Superfamily:   Thiamin diphosphate-binding fold (THDP-binding) [ 52518] (8)
Families:   Pyruvate oxidase and decarboxylase Pyr module [ 88724] (8)
  TK-like Pyr module [ 88735] (2)
  Branched-chain alpha-keto acid dehydrogenase Pyr module [ 88741] (4)
  PFOR Pyr module [ 88746]
  Pyruvate oxidase and decarboxylase PP module [ 88749] (8)
  TK-like PP module [ 88760] (2)
  Branched-chain alpha-keto acid dehydrogenase PP module [ 88766] (4)
  PFOR PP module [ 88771]


Superfamily statistics
Genomes (3,228) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 64,819 369,622 92
Proteins 40,048 231,964 60


Functional annotation
General category General
Detailed category Small molecule binding

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 process0.00000000036170Least InformativeDirect
Biological Process (BP)single-organism cellular process0.0000014270Least InformativeDirect
Biological Process (BP)biosynthetic process0.0057970.0006986Least InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.000000000010650Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process0.000000000087080Moderately InformativeDirect
Biological Process (BP)monocarboxylic acid metabolic process0.0033870.001328Moderately InformativeInherited
Biological Process (BP)coenzyme biosynthetic process0.0000062970.00000000001635InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process00InformativeDirect
Biological Process (BP)acyl-CoA biosynthetic process0.000000061340Highly InformativeDirect
Molecular Function (MF)binding0.46091Least InformativeInherited
Molecular Function (MF)oxidoreductase activity0.0000000014830Moderately InformativeDirect
Molecular Function (MF)lyase activity0.0077990.000000004753Moderately InformativeInherited
Molecular Function (MF)anion binding0.032330.06399Moderately InformativeInherited
Molecular Function (MF)small molecule binding0.06710.00000782Moderately InformativeInherited
Molecular Function (MF)carbon-carbon lyase activity0.000000053630InformativeDirect
Molecular Function (MF)coenzyme binding0.000052350InformativeDirect
Molecular Function (MF)sulfur compound binding0.000030040InformativeDirect
Molecular Function (MF)carboxy-lyase activity0.000000000023430.00002073Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the aldehyde or oxo group of donors0.000000000016950Highly InformativeDirect
Molecular Function (MF)vitamin binding0.00002630Highly InformativeDirect
Cellular Component (CC)macromolecular complex0.0019560.0000002393Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.20080Least InformativeInherited
Cellular Component (CC)cytosolic part0.00013770.05504Moderately InformativeInherited
Cellular Component (CC)oxidoreductase complex0.0000000000082530InformativeDirect

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 0.0006986 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.0000000001953 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.0000001947 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.000000001011 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.7196 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.001328 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.1811 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.2317 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.06664 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.8443 Moderately Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0.000000000000001945 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 0.00000000001635 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0 Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 0 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.1133 Informative Inherited
Biological Process (BP) cellular respiration 0.9342 Informative Inherited
Biological Process (BP) system process 1 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.5682 Informative Inherited
Biological Process (BP) fatty acid metabolic process 1 Informative Inherited
Biological Process (BP) cellular lipid catabolic process 0.1244 Informative Inherited
Biological Process (BP) alcohol metabolic process 1 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.03499 Informative Inherited
Biological Process (BP) citrate metabolic process 0 Highly Informative Direct
Biological Process (BP) fermentation 0.000007112 Highly Informative Direct
Biological Process (BP) NADP metabolic process 0.0004561 Highly Informative Direct
Biological Process (BP) aerobic respiration 0.000000009446 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0 Highly Informative Direct
Biological Process (BP) glyceraldehyde-3-phosphate metabolic process 0 Highly Informative Direct
Biological Process (BP) glucose 6-phosphate metabolic process 0 Highly Informative Direct
Biological Process (BP) heart contraction 0.0001595 Highly Informative Direct
Biological Process (BP) acyl-CoA biosynthetic process 0 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.09446 Highly Informative Inherited
Biological Process (BP) lipid modification 0.0184 Highly Informative Inherited
Biological Process (BP) alcohol biosynthetic process 0.04462 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.000000004753 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.00000782 Moderately Informative Direct
Molecular Function (MF) anion binding 0.06399 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 1 Moderately Informative Inherited
Molecular Function (MF) magnesium ion binding 0.000001483 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) coenzyme binding 0 Informative Direct
Molecular Function (MF) sulfur compound binding 0 Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.00002073 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the aldehyde or oxo group of donors 0 Highly Informative Direct
Molecular Function (MF) vitamin binding 0 Highly Informative Direct
Cellular Component (CC) macromolecular complex 0.0000002393 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0003931 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) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0 Moderately Informative Direct
Cellular Component (CC) transferase complex 1 Moderately Informative Inherited
Cellular Component (CC) cytosolic part 0.05504 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.01191 Moderately Informative Inherited
Cellular Component (CC) oxidoreductase complex 0 Informative Direct
Cellular Component (CC) external encapsulating structure 0.003223 Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0.00000000004878Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0.000002754Moderately InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor0Highly InformativeDirect
Enzyme Commission (EC)In ketonic substances1Highly InformativeInherited
Enzyme Commission (EC)Transketolases and transaldolases1Highly InformativeInherited

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 the musculature0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.1983Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of muscle physiology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.0002091Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of higher mental function0.1934Moderately InformativeInherited
Phenotypic Abnormality (PA)Muscular hypotonia0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of amino acid metabolism0.00006933InformativeDirect
Phenotypic Abnormality (PA)Lethargy0.0002086InformativeDirect
Phenotypic Abnormality (PA)Lactic acidosis0.0000001188Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.08174Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.3509Least InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.007456Moderately InformativeInherited
Worm Phenotype (WP)level of transgene expression variant0.008761Moderately InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.0265Moderately InformativeInherited
Worm Phenotype (WP)life span variant0.0001766InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.0004351InformativeDirect
Worm Phenotype (WP)transgene expression increased0.0008452InformativeDirect
Worm Phenotype (WP)body length variant0.006221InformativeInherited
Worm Phenotype (WP)body width variant0.008081InformativeInherited
Worm Phenotype (WP)small0.0003025Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited

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)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0.1395Least InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.01067Moderately InformativeInherited
Xenopus ANatomical entity (XAN)pancreas0.00000009791InformativeDirect
Xenopus ANatomical entity (XAN)heart0.000005766InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)seed development stage0.0008028InformativeDirect

Document: AP 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)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases0.000005559Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Acyl groups converted into alkyl groups on transfer0.2821Highly InformativeInherited
Enzyme Commission (EC)Transketolases and transaldolases1Highly InformativeInherited
Enzyme Commission (EC)In ketonic substances1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCarbohydrate metabolism0.7843Moderately InformativeInherited
Biological processAmino-acid biosynthesis1Moderately InformativeInherited
Biological processGlycolysis0InformativeDirect
Biological processTricarboxylic acid cycle0.00000000000003367InformativeDirect
Biological processNitrogen fixation0.0004928InformativeDirect
Biological processGlucose metabolism0Highly InformativeDirect
Biological processIsoprene biosynthesis0Highly InformativeDirect
Biological processMenaquinone biosynthesis0Highly InformativeDirect
Biological processThiamine biosynthesis0Highly InformativeDirect
Biological processBranched-chain amino acid biosynthesis0.00000000000002001Highly InformativeDirect
Cellular componentMitochondrion0.0000000000005103Moderately InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionCalcium0.0000000000197Moderately InformativeDirect
Molecular functionFlavoprotein0.5418Moderately InformativeInherited
Molecular functionFAD0.0000000006814InformativeDirect
Molecular functionPyruvate0Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase0.000001862Moderately InformativeDirect
Post-translational modificationDecarboxylase0Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cofactor metabolism0.00000000001943Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis0Moderately InformativeDirect
UniPathway (UP)alcohol metabolism0.00007189Moderately InformativeDirect
UniPathway (UP)carbohydrate biosynthesis0.757Moderately InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis1Moderately InformativeInherited
UniPathway (UP)energy metabolism1Moderately InformativeInherited
UniPathway (UP)amino-acid degradation1Moderately InformativeInherited
UniPathway (UP)quinol/quinone biosynthesis0InformativeDirect
UniPathway (UP)L-isoleucine biosynthesis0.0000000000003118InformativeDirect
UniPathway (UP)organosulfur metabolism0.000005355InformativeDirect
UniPathway (UP)alcohol degradation0.02132InformativeInherited
UniPathway (UP)alcohol biosynthesis0.7692InformativeInherited
UniPathway (UP)myo-inositol degradation into acetyl-CoA0Highly InformativeDirect
UniPathway (UP)menaquinone biosynthesis0Highly InformativeDirect
UniPathway (UP)L-valine biosynthesis0.00000000000008197Highly InformativeDirect
UniPathway (UP)organosulfur degradation0.000000004352Highly InformativeDirect
UniPathway (UP)coenzyme M biosynthesis0.00000007284Highly InformativeDirect
UniPathway (UP)Calvin cycle0.0000001825Highly InformativeDirect
UniPathway (UP)(R,R)-butane-2,3-diol metabolism0.000831Highly InformativeDirect
UniPathway (UP)polyol biosynthesis0.201Highly InformativeInherited
UniPathway (UP)ketone degradation1Highly InformativeInherited

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) · Worm Phenotype (WP) · 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 45 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 Thiamin diphosphate-binding fold (THDP-binding) 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 45 hidden Markov models representing the Thiamin diphosphate-binding fold (THDP-binding) 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) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]