SUPERFAMILY 1.75 HMM library and genome assignments server

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 (3,222) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 64,711 346,064 92
Proteins 39,981 211,801 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 process0.00055420Least InformativeDirect
Biological Process (BP)biosynthetic process0.54980.001901Least InformativeInherited
Biological Process (BP)cofactor metabolic process0.00015090Moderately InformativeDirect
Biological Process (BP)monocarboxylic acid metabolic process0.036760.04488Moderately InformativeInherited
Biological Process (BP)coenzyme biosynthetic process0.0000035640.0009185InformativeDirect
Biological Process (BP)acyl-CoA metabolic process0.0000000013780Highly InformativeDirect
Biological Process (BP)thioester biosynthetic process0.0000000000077740Highly InformativeDirect
Molecular Function (MF)lyase activity0.000011190.0000000000002139Moderately InformativeDirect
Molecular Function (MF)oxidoreductase activity0.0011870Moderately InformativeInherited
Molecular Function (MF)oxidoreductase activity, acting on the aldehyde or oxo group of donors0.0000017180Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.062250.008647Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.040440Least InformativeInherited
Cellular Component (CC)microbody0.0000001180.000000007557InformativeDirect

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 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.9104 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.001901 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) cellular component organization or biogenesis 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) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.00000000000008478 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.000008749 Moderately Informative Direct
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.9969 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.01543 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.2321 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.3732 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.04488 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.3219 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.09504 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.002824 Moderately Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0.0009185 Informative Direct
Biological Process (BP) carbohydrate catabolic process 0.000000007735 Informative Direct
Biological Process (BP) hexose metabolic process 0 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) response to inorganic substance 0.2665 Informative Inherited
Biological Process (BP) cellular biogenic amine metabolic process 1 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.5588 Informative Inherited
Biological Process (BP) microtubule-based process 0.2255 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.6669 Informative Inherited
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.8516 Informative Inherited
Biological Process (BP) energy derivation by oxidation of organic compounds 0.005681 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.6308 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.1817 Informative Inherited
Biological Process (BP) alcohol metabolic process 1 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.007566 Informative Inherited
Biological Process (BP) acyl-CoA metabolic process 0 Highly Informative Direct
Biological Process (BP) aerobic respiration 0.0000006453 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0 Highly Informative Direct
Biological Process (BP) pentose metabolic process 0.0001419 Highly Informative Direct
Biological Process (BP) primary alcohol metabolic process 0.000002409 Highly Informative Direct
Biological Process (BP) thioester biosynthetic process 0 Highly Informative Direct
Biological Process (BP) cellular biogenic amine catabolic process 0.0001392 Highly Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) response to cadmium ion 0.0001078 Highly Informative Direct
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 0.0000000000002139 Moderately Informative Direct
Molecular Function (MF) cation binding 0.00001721 Moderately Informative Direct
Molecular Function (MF) anion binding 0.3634 Moderately Informative Inherited
Molecular Function (MF) magnesium ion binding 0.00005226 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.0000000003539 Informative Direct
Molecular Function (MF) cofactor binding 0.00000000003318 Informative Direct
Molecular Function (MF) sulfur compound binding 0.00000000003465 Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.0006716 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the aldehyde or oxo group of donors 0 Highly Informative Direct
Cellular Component (CC) protein complex 0.00000006516 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.008647 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.9185 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.0000000002524 Moderately Informative Direct
Cellular Component (CC) cytosol 1 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.1426 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.7427 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 0 Informative Direct
Cellular Component (CC) external encapsulating structure 0.0005868 Informative Direct
Cellular Component (CC) microbody 0.000000007557 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.07897 Informative Inherited
Cellular Component (CC) microtubule associated complex 0.0004568 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)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 nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.001123Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.07756Moderately InformativeInherited
Phenotypic Abnormality (PA)Lethargy0.00008008InformativeDirect
Phenotypic Abnormality (PA)Abnormality of carboxylic acid metabolism0.0004277InformativeDirect
Phenotypic Abnormality (PA)Abnormality of coordination0.000888InformativeDirect
Phenotypic Abnormality (PA)Abnormality of pyramidal motor function0.00391InformativeInherited
Phenotypic Abnormality (PA)Lactic acidosis0.000001186Highly InformativeDirect
Phenotypic Abnormality (PA)Hypertonia0.0007292Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)growth/size/body phenotype0Least InformativeDirect
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0Moderately InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)life span variant0.0002996InformativeDirect

Document: WP 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)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)intestine0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)heart0InformativeDirect
Xenopus ANatomical entity (XAN)pancreas0.0000002826Highly InformativeDirect

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 stage0.0008019InformativeDirect

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 lyases0.00003225Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0.00000002615InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Acyl groups converted into alkyl on transfer0.4672Highly 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 metabolism0.7968Moderately InformativeInherited
Biological processAmino-acid biosynthesis1Moderately InformativeInherited
Biological processGlycolysis0InformativeDirect
Biological processTricarboxylic acid cycle0.00000000000006719InformativeDirect
Biological processNitrogen fixation0.0006454InformativeDirect
Biological processGlucose metabolism0Highly InformativeDirect
Biological processIsoprene biosynthesis0Highly InformativeDirect
Biological processMenaquinone biosynthesis0Highly InformativeDirect
Biological processThiamine biosynthesis0Highly InformativeDirect
Biological processBranched-chain amino acid biosynthesis0.00000000000002144Highly InformativeDirect
Cellular componentMitochondrion0.0000000000002067Moderately InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionCalcium4.62e-16Moderately InformativeDirect
Molecular functionFlavoprotein0.01475Moderately InformativeInherited
Molecular functionFAD0.00000000001181InformativeDirect
Molecular functionPyruvate0Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase0.00001451Moderately InformativeDirect
Post-translational modificationDecarboxylase0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cofactor metabolism0.0000000001031Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis0Moderately InformativeDirect
UniPathway (UP)alcohol metabolism0.00003801Moderately InformativeDirect
UniPathway (UP)carbohydrate biosynthesis0.743Moderately InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis1Moderately InformativeInherited
UniPathway (UP)energy metabolism1Moderately InformativeInherited
UniPathway (UP)amino-acid degradation1Moderately InformativeInherited
UniPathway (UP)quinone cofactor biosynthesis0InformativeDirect
UniPathway (UP)L-isoleucine biosynthesis0.0000000000002401InformativeDirect
UniPathway (UP)polyol degradation0.005491InformativeInherited
UniPathway (UP)alcohol biosynthesis0.7957InformativeInherited
UniPathway (UP)myo-inositol degradation into acetyl-CoA0Highly InformativeDirect
UniPathway (UP)menaquinone biosynthesis0Highly InformativeDirect
UniPathway (UP)L-valine biosynthesis0.00000000000007513Highly InformativeDirect
UniPathway (UP)organosulfur degradation0.0000001005Highly InformativeDirect
UniPathway (UP)Calvin cycle0.0000001784Highly InformativeDirect
UniPathway (UP)coenzyme M biosynthesis0.000009975Highly InformativeDirect
UniPathway (UP)(R,R)-butane-2,3-diol metabolism0.0009693Highly InformativeDirect
UniPathway (UP)polyol biosynthesis0.2235Highly 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]