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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 (3,230) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 64,974 369,622 92
Proteins 40,163 231,964 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 process0.00000000026020Least InformativeDirect
Biological Process (BP)single-organism cellular process0.0000013360Least InformativeDirect
Biological Process (BP)biosynthetic process0.0054850.000375Least InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.0000000000089070Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process0.000000000066520Moderately InformativeDirect
Biological Process (BP)monocarboxylic acid metabolic process0.0032610.001919Moderately InformativeInherited
Biological Process (BP)coenzyme biosynthetic process0.0000060610.0000000000135InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process00InformativeDirect
Biological Process (BP)acyl-CoA biosynthetic process0.000000061390Highly InformativeDirect
Molecular Function (MF)binding0.41411Least InformativeInherited
Molecular Function (MF)oxidoreductase activity0.000000001490Moderately InformativeDirect
Molecular Function (MF)lyase activity0.0078210.000000001367Moderately InformativeInherited
Molecular Function (MF)small molecule binding0.078950.000006744Moderately InformativeInherited
Molecular Function (MF)anion binding0.033520.05754Moderately InformativeInherited
Molecular Function (MF)carbon-carbon lyase activity0.000000055110InformativeDirect
Molecular Function (MF)coenzyme binding0.000056330InformativeDirect
Molecular Function (MF)sulfur compound binding0.000040160InformativeDirect
Molecular Function (MF)carboxy-lyase activity0.000000000024790.00006876Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the aldehyde or oxo group of donors0.000000000017870Highly InformativeDirect
Molecular Function (MF)vitamin binding0.000028140Highly InformativeDirect
Cellular Component (CC)cytoplasmic part0.21820Least InformativeInherited
Cellular Component (CC)cytosolic part0.00012670.04946Moderately InformativeInherited
Cellular Component (CC)oxidoreductase complex0.000000000012810InformativeDirect

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 0.000375 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) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound 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 0.00000000001838 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.0000001671 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 0.000000001008 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.7632 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.303 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.001919 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.2454 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.7229 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.07002 Moderately Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0.000000000000001925 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 0.0000000000135 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) system process 1 Informative Inherited
Biological Process (BP) oxidoreduction coenzyme metabolic process 1 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.1125 Informative Inherited
Biological Process (BP) cellular respiration 0.8993 Informative Inherited
Biological Process (BP) fatty acid metabolic process 1 Informative Inherited
Biological Process (BP) lipid catabolic process 0.1849 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.5955 Informative Inherited
Biological Process (BP) alcohol metabolic process 1 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.04 Informative Inherited
Biological Process (BP) citrate metabolic process 0 Highly Informative Direct
Biological Process (BP) fermentation 0.00000651 Highly Informative Direct
Biological Process (BP) NADP metabolic process 0.0003875 Highly Informative Direct
Biological Process (BP) aerobic respiration 0.000000009728 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 0.00002532 Highly Informative Direct
Biological Process (BP) acyl-CoA biosynthetic process 0 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.09564 Highly Informative Inherited
Biological Process (BP) lipid modification 0.0184 Highly Informative Inherited
Biological Process (BP) alcohol biosynthetic process 0.0617 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 0.000000001367 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.000006744 Moderately Informative Direct
Molecular Function (MF) anion binding 0.05754 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 1 Moderately Informative Inherited
Molecular Function (MF) magnesium ion binding 0.00000146 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 0.00006876 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) intracellular membrane-bounded organelle 0.0002585 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) mitochondrial protein complex 0 Moderately Informative Direct
Cellular Component (CC) transferase complex 1 Moderately Informative Inherited
Cellular Component (CC) cytosolic part 0.04946 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.009544 Moderately Informative Inherited
Cellular Component (CC) oxidoreductase complex 0 Informative Direct
Cellular Component (CC) external encapsulating structure 0.0029 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCarbohydrate metabolism0.7961Moderately InformativeInherited
Biological processAmino-acid biosynthesis1Moderately InformativeInherited
Biological processGlycolysis0InformativeDirect
Biological processTricarboxylic acid cycle0.00000000000003188InformativeDirect
Biological processNitrogen fixation0.0004847InformativeDirect
Biological processIsoprene biosynthesis0Highly InformativeDirect
Biological processThiamine biosynthesis0Highly InformativeDirect
Biological processGlucose metabolism0Highly InformativeDirect
Biological processMenaquinone biosynthesis0Highly InformativeDirect
Biological processBranched-chain amino acid biosynthesis0.00000000000001865Highly InformativeDirect
Cellular componentMitochondrion0.0000000000005622Moderately InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionCalcium0.00000000002347Moderately InformativeDirect
Molecular functionFlavoprotein0.5425Moderately InformativeInherited
Molecular functionFAD0.0000000007148InformativeDirect
Molecular functionPyruvate0Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase0.000002276Moderately InformativeDirect
Post-translational modificationDecarboxylase0Highly InformativeDirect

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 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) · UniProtKB KeyWords (KW) · Internal database links ]