SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 (3,223) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 64,729 346,064 92
Proteins 39,991 211,801 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 process0.00000000069680Least InformativeDirect
Biological Process (BP)single-organism cellular process0.00001910Least InformativeDirect
Biological Process (BP)biosynthetic process0.0072240.001003Least InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.000000000010920Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process0.00000000008530Moderately InformativeDirect
Biological Process (BP)monocarboxylic acid metabolic process0.0036110.0005766Moderately InformativeInherited
Biological Process (BP)coenzyme biosynthetic process0.0000080010.00000000001475InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process00InformativeDirect
Biological Process (BP)acyl-CoA biosynthetic process0.00000019430Highly InformativeDirect
Molecular Function (MF)binding0.92021Least InformativeInherited
Molecular Function (MF)oxidoreductase activity0.0000000016490Moderately InformativeDirect
Molecular Function (MF)anion binding0.016510.07865Moderately InformativeInherited
Molecular Function (MF)small molecule binding0.010520.00000222Moderately InformativeInherited
Molecular Function (MF)lyase activity0.0074330.000000003879Moderately InformativeInherited
Molecular Function (MF)carbon-carbon lyase activity0.000000013440InformativeDirect
Molecular Function (MF)coenzyme binding0.000015880InformativeDirect
Molecular Function (MF)sulfur compound binding0.000005210InformativeDirect
Molecular Function (MF)carboxy-lyase activity0.0000000000056940.00003045Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the aldehyde or oxo group of donors0.000000000017290Highly InformativeDirect
Cellular Component (CC)cytoplasmic part0.10520Least InformativeInherited
Cellular Component (CC)cytosolic part0.0001030.05602Moderately InformativeInherited
Cellular Component (CC)oxidoreductase complex0.0000000000018350InformativeDirect

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) single-organism cellular process 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0007341 Least Informative Direct
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.001003 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic 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) generation of precursor metabolites and energy 0 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.0000000001276 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.0000002275 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) ribose phosphate metabolic process 0.0000007886 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.0005766 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.0000000009477 Moderately Informative Direct
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.7151 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.07018 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.07484 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.07642 Moderately Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 0.00000000001475 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 0.9339 Informative Inherited
Biological Process (BP) oxidoreduction coenzyme metabolic process 1 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.8873 Informative Inherited
Biological Process (BP) microtubule-based process 0.8788 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.2191 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.3834 Informative Inherited
Biological Process (BP) cellular respiration 0.9753 Informative Inherited
Biological Process (BP) fatty acid metabolic process 1 Informative Inherited
Biological Process (BP) lipid catabolic process 0.1738 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.002025 Informative Inherited
Biological Process (BP) alcohol metabolic process 1 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.02547 Informative Inherited
Biological Process (BP) citrate metabolic process 0 Highly Informative Direct
Biological Process (BP) fermentation 0.000009681 Highly Informative Direct
Biological Process (BP) aerobic respiration 0.00000000705 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 0.0001064 Highly Informative Direct
Biological Process (BP) acyl-CoA biosynthetic process 0 Highly Informative Direct
Biological Process (BP) microtubule cytoskeleton organization 0.05924 Highly Informative Inherited
Biological Process (BP) NADP metabolic process 0.001521 Highly Informative Inherited
Biological Process (BP) fatty acid catabolic process 0.08198 Highly Informative Inherited
Biological Process (BP) lipid modification 0.01788 Highly Informative Inherited
Biological Process (BP) alcohol biosynthetic process 0.05045 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 0.000000003879 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.00000222 Moderately Informative Direct
Molecular Function (MF) anion binding 0.07865 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 1 Moderately Informative Inherited
Molecular Function (MF) magnesium ion binding 0.000004106 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 0.00003045 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the aldehyde or oxo group of donors 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0001528 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.8073 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) cytosolic part 0.05602 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.02025 Moderately Informative Inherited
Cellular Component (CC) transferase complex 1 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.8013 Moderately Informative Inherited
Cellular Component (CC) lipid particle 0.0005811 Informative Direct
Cellular Component (CC) oxidoreductase complex 0 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.1409 Informative Inherited
Cellular Component (CC) external encapsulating structure 0.00198 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 physiology0.2206Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of muscle physiology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.0002009Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of higher mental function0.176Moderately InformativeInherited
Phenotypic Abnormality (PA)Muscular hypotonia0InformativeDirect
Phenotypic Abnormality (PA)Acidosis0.000003697InformativeDirect
Phenotypic Abnormality (PA)Abnormality of amino acid metabolism0.00007221InformativeDirect
Phenotypic Abnormality (PA)Lethargy0.0002059InformativeDirect
Phenotypic Abnormality (PA)Lactic acidosis0.0000001134Highly 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 region phenotype0Least InformativeDirect

Document: MP 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 variant0.07904Least InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.007247Moderately InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.02611Moderately InformativeInherited
Worm Phenotype (WP)life span variant0.0001326InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.0004402InformativeDirect
Worm Phenotype (WP)body length variant0.006083InformativeInherited
Worm Phenotype (WP)body width variant0.007992InformativeInherited
Worm Phenotype (WP)small0.0002928Highly InformativeDirect

Document: WP 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 cluster0.1407Least InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.01053Moderately InformativeInherited
Xenopus ANatomical entity (XAN)pancreas0.00000009935InformativeDirect
Xenopus ANatomical entity (XAN)heart0.000005602InformativeDirect
Xenopus ANatomical entity (XAN)kidney0.001379InformativeInherited

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 lyases0.000007714Moderately 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 transfer0.2872Highly 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 metabolism0.7846Moderately InformativeInherited
Biological processAmino-acid biosynthesis1Moderately InformativeInherited
Biological processGlycolysis0InformativeDirect
Biological processTricarboxylic acid cycle0.00000000000003592InformativeDirect
Biological processNitrogen fixation0.0004927InformativeDirect
Biological processGlucose metabolism0Highly InformativeDirect
Biological processIsoprene biosynthesis0Highly InformativeDirect
Biological processMenaquinone biosynthesis0Highly InformativeDirect
Biological processThiamine biosynthesis0Highly InformativeDirect
Biological processBranched-chain amino acid biosynthesis0.00000000000002132Highly InformativeDirect
Cellular componentMitochondrion0.0000000000004543Moderately InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionCalcium4.676e-16Moderately InformativeDirect
Molecular functionFAD0.0000000006393InformativeDirect
Molecular functionPyruvate0Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase0.00001195Moderately 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 metabolism0.00000000001566Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis0Moderately InformativeDirect
UniPathway (UP)alcohol metabolism0.00006134Moderately InformativeDirect
UniPathway (UP)carbohydrate biosynthesis0.7613Moderately 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 biosynthesis0.0000000000003196InformativeDirect
UniPathway (UP)organosulfur metabolism0.000003693InformativeDirect
UniPathway (UP)alcohol degradation0.02349InformativeInherited
UniPathway (UP)alcohol biosynthesis0.7756InformativeInherited
UniPathway (UP)myo-inositol degradation into acetyl-CoA0Highly InformativeDirect
UniPathway (UP)menaquinone biosynthesis0Highly InformativeDirect
UniPathway (UP)L-valine biosynthesis0.00000000000008375Highly InformativeDirect
UniPathway (UP)organosulfur degradation0.00000000441Highly InformativeDirect
UniPathway (UP)coenzyme M biosynthesis0.00000007363Highly InformativeDirect
UniPathway (UP)Calvin cycle0.0000001873Highly InformativeDirect
UniPathway (UP)(R,R)-butane-2,3-diol metabolism0.0008728Highly InformativeDirect
UniPathway (UP)polyol biosynthesis0.2082Highly 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 ]