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 (3,230) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 64,974 496,707 92
Proteins 40,163 311,713 60


Functional annotation
General category General
Detailed category Small molecule binding

Document:
Function annotation of SCOP domain superfamilies

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 the musculature0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.03608Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.197Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal muscle tone0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.00003839Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of higher mental function0.2823Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal circulating metabolite concentration0.4783Moderately InformativeInherited
Phenotypic Abnormality (PA)Muscular hypotonia0InformativeDirect
Phenotypic Abnormality (PA)Acidosis0.00002133InformativeDirect
Phenotypic Abnormality (PA)Abnormality of serum amino acid level0.0004InformativeDirect
Phenotypic Abnormality (PA)Reduced consciousness/confusion0.01627InformativeInherited
Phenotypic Abnormality (PA)Generalized hypotonia0Highly InformativeDirect
Phenotypic Abnormality (PA)Lactic acidosis0.0000002905Highly InformativeDirect
Phenotypic Abnormality (PA)Lethargy0.0007595Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.1387Least InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.004361Moderately InformativeInherited
Worm Phenotype (WP)body region morphology variant0.01Moderately InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.01Moderately InformativeInherited
Worm Phenotype (WP)developmental morphology variant0.01003Moderately InformativeInherited
Worm Phenotype (WP)adult body morphology variant0.01006Moderately InformativeInherited
Worm Phenotype (WP)body morphology variant0.01082Moderately InformativeInherited
Worm Phenotype (WP)avoids bacterial lawn0.0004322InformativeDirect
Worm Phenotype (WP)small0.0008572InformativeDirect

Document: WP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)adult0Least InformativeDirect
Fly Anatomy (FA)nervous system0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)head0Moderately InformativeDirect
Fly Anatomy (FA)peripheral nervous system0Moderately InformativeDirect
Fly Anatomy (FA)sensory system0Moderately InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)trunk0Least InformativeDirect
Xenopus ANatomical entity (XAN)cavitated compound organ0Least InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0.009212Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.03649Moderately InformativeInherited
Xenopus ANatomical entity (XAN)pancreas0.00000022Highly 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 lyases0.000003459Moderately InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups1Moderately InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0.00000001275InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Acyl groups converted into alkyl groups on transfer0.1655Highly InformativeInherited
Enzyme Commission (EC)Transketolases and transaldolases1Highly InformativeInherited
Enzyme Commission (EC)In ketonic substances1Highly InformativeInherited

Document: EC annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 57 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 57 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]