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 (3,215) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 64,469 346,064 92
Proteins 39,792 211,801 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 process0.00097880Least InformativeDirect
Biological Process (BP)biosynthetic process0.44570.001966Least InformativeInherited
Biological Process (BP)cofactor metabolic process7.609e-050Moderately InformativeDirect
Biological Process (BP)monocarboxylic acid metabolic process0.00036260.0165Moderately InformativeInherited
Biological Process (BP)coenzyme biosynthetic process1.726e-060.0007192InformativeDirect
Biological Process (BP)acyl-CoA metabolic process7.085e-100Highly InformativeDirect
Biological Process (BP)thioester biosynthetic process4.749e-120Highly InformativeDirect
Molecular Function (MF)lyase activity2.941e-061.322e-13Moderately InformativeDirect
Molecular Function (MF)oxidoreductase activity0.0099320Moderately InformativeInherited
Molecular Function (MF)oxidoreductase activity, acting on the aldehyde or oxo group of donors9.97e-050Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.033380.01133Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.038230Least InformativeInherited
Cellular Component (CC)microbody1.183e-075.837e-09InformativeDirect

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 0.8525 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.001966 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 3.063e-13 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 3.722e-15 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 9.3e-06 Moderately Informative Direct
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.9715 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.009451 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.2284 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.3821 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.0165 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.3741 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.07006 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.001707 Moderately Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0.0007192 Informative Direct
Biological Process (BP) carbohydrate catabolic process 3.722e-09 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 0.239 Informative Inherited
Biological Process (BP) cellular biogenic amine metabolic process 1 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.525 Informative Inherited
Biological Process (BP) microtubule-based process 0.21 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.7307 Informative Inherited
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.8904 Informative Inherited
Biological Process (BP) energy derivation by oxidation of organic compounds 0.006775 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.2235 Informative Inherited
Biological Process (BP) alcohol metabolic process 1 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.006045 Informative Inherited
Biological Process (BP) acyl-CoA metabolic process 0 Highly Informative Direct
Biological Process (BP) aerobic respiration 1.332e-06 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0 Highly Informative Direct
Biological Process (BP) pentose metabolic process 0.0001243 Highly Informative Direct
Biological Process (BP) thioester biosynthetic process 0 Highly Informative Direct
Biological Process (BP) cellular biogenic amine catabolic process 0.0001359 Highly Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) response to cadmium ion 9.579e-05 Highly Informative Direct
Biological Process (BP) microtubule cytoskeleton organization 0.06341 Highly Informative Inherited
Biological Process (BP) alcohol biosynthetic process 0.0375 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) lyase activity 1.322e-13 Moderately Informative Direct
Molecular Function (MF) anion binding 0.1765 Moderately Informative Inherited
Molecular Function (MF) cation binding 0.001652 Moderately Informative Inherited
Molecular Function (MF) carbon-carbon lyase activity 1.167e-09 Informative Direct
Molecular Function (MF) cofactor binding 1.081e-09 Informative Direct
Molecular Function (MF) sulfur compound binding 4.078e-08 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the aldehyde or oxo group of donors 0 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.001096 Highly Informative Inherited
Cellular Component (CC) protein complex 8.475e-08 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.01133 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.87 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 1.612e-10 Moderately Informative Direct
Cellular Component (CC) cytosol 1 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.1572 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.7117 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 0 Informative Direct
Cellular Component (CC) microbody 5.837e-09 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.07461 Informative Inherited
Cellular Component (CC) microtubule associated complex 0.0004545 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)Oxidoreductases4.878e-11Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases2.754e-06Moderately 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 homeostasis0.001097Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.07947Moderately InformativeInherited
Phenotypic Abnormality (PA)Lethargy8.544e-05InformativeDirect
Phenotypic Abnormality (PA)Abnormality of carboxylic acid metabolism0.0004218InformativeDirect
Phenotypic Abnormality (PA)Abnormality of coordination0.0009344InformativeDirect
Phenotypic Abnormality (PA)Abnormality of pyramidal motor function0.003931InformativeInherited
Phenotypic Abnormality (PA)Lactic acidosis1.098e-06Highly InformativeDirect
Phenotypic Abnormality (PA)Hypertonia0.0007512Highly 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)pancreas2.82e-07Highly 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)Oxidoreductases2.419e-16Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases2.031e-05Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0InformativeDirect
Enzyme Commission (EC)Carboxy-lyases1.936e-08InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Acyl groups converted into alkyl on transfer0.4637Highly 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 metabolism0.7881Moderately InformativeInherited
Biological processAmino-acid biosynthesis1Moderately InformativeInherited
Biological processGlycolysis0InformativeDirect
Biological processTricarboxylic acid cycle6.309e-14InformativeDirect
Biological processNitrogen fixation0.0006428InformativeDirect
Biological processGlucose metabolism0Highly InformativeDirect
Biological processIsoprene biosynthesis0Highly InformativeDirect
Biological processMenaquinone biosynthesis0Highly InformativeDirect
Biological processThiamine biosynthesis0Highly InformativeDirect
Biological processBranched-chain amino acid biosynthesis1.94e-14Highly InformativeDirect
Cellular componentMitochondrion1.661e-13Moderately InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionCalcium4.636e-16Moderately InformativeDirect
Molecular functionFlavoprotein0.01334Moderately InformativeInherited
Molecular functionFAD9.012e-12InformativeDirect
Molecular functionPyruvate0Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase1.587e-05Moderately 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 metabolism1.505e-10Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis0Moderately InformativeDirect
UniPathway (UP)alcohol metabolism2.996e-05Moderately InformativeDirect
UniPathway (UP)carbohydrate biosynthesis0.7389Moderately 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 biosynthesis2.396e-13InformativeDirect
UniPathway (UP)polyol degradation0.007302InformativeInherited
UniPathway (UP)alcohol biosynthesis0.8047InformativeInherited
UniPathway (UP)myo-inositol degradation into acetyl-CoA0Highly InformativeDirect
UniPathway (UP)menaquinone biosynthesis0Highly InformativeDirect
UniPathway (UP)L-valine biosynthesis7.488e-14Highly InformativeDirect
UniPathway (UP)organosulfur degradation1.008e-07Highly InformativeDirect
UniPathway (UP)Calvin cycle1.794e-07Highly InformativeDirect
UniPathway (UP)coenzyme M biosynthesis9.823e-06Highly InformativeDirect
UniPathway (UP)(R,R)-butane-2,3-diol metabolism0.001027Highly InformativeInherited
UniPathway (UP)polyol biosynthesis0.2252Highly 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 ]