SUPERFAMILY 1.75 HMM library and genome assignments server


Phosphoenolpyruvate/pyruvate domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   TIM beta/alpha-barrel [ 51350] (33)
Superfamily:   Phosphoenolpyruvate/pyruvate domain [ 51621] (7)
Families:   Pyruvate kinase [ 51622]
  Pyruvate phosphate dikinase, C-terminal domain [ 51629]
  Phosphoenolpyruvate carboxylase [ 51632]
  Phosphoenolpyruvate mutase/Isocitrate lyase-like [ 88704] (3)
  HpcH/HpaI aldolase [ 51638] (3)
  Ketopantoate hydroxymethyltransferase PanB [ 89503]
  Mll9387-like [ 159416]


Superfamily statistics
Genomes (3,209) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 23,303 0 43
Proteins 23,210 0 43


Functional annotation
General category Metabolism
Detailed category Energy

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 process6.517e-057.575e-08Least InformativeDirect
Biological Process (BP)biosynthetic process0.99430.6972Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process0.63280.2902Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.016780.05707Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.15680.1207Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.63540.8604Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.83030.003472Moderately InformativeInherited
Biological Process (BP)cellular lipid metabolic process0.69140.4328Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.00058930.005398Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.037580.03915Moderately InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.0044970.1167Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.0020410Moderately InformativeInherited
Biological Process (BP)cellular modified amino acid metabolic process0.00089846.508e-05InformativeDirect
Biological Process (BP)vitamin metabolic process0.00030770.0002569InformativeDirect
Biological Process (BP)coenzyme biosynthetic process2.797e-066.9e-07InformativeDirect
Biological Process (BP)cellular amide metabolic process3.721e-061.052e-05InformativeDirect
Biological Process (BP)cellular carbohydrate metabolic process1.381e-052.103e-05InformativeDirect
Biological Process (BP)carboxylic acid catabolic process0.74960.9167InformativeInherited
Biological Process (BP)lipid catabolic process0.0086340.02673InformativeInherited
Biological Process (BP)fatty acid metabolic process0.33030.3625InformativeInherited
Biological Process (BP)cellular modified amino acid biosynthetic process3.82e-091.007e-09Highly InformativeDirect
Biological Process (BP)amide biosynthetic process1.246e-071.296e-08Highly InformativeDirect
Biological Process (BP)glyoxylate metabolic process7.163e-120Highly InformativeDirect
Biological Process (BP)fatty acid catabolic process0.00065830.002967Highly InformativeInherited
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)lyase activity00Moderately InformativeDirect
Molecular Function (MF)cation binding9.853e-062.119e-06Moderately InformativeDirect
Molecular Function (MF)carbon-carbon lyase activity00InformativeDirect
Molecular Function (MF)transferase activity, transferring one-carbon groups5.262e-060.0705InformativeInherited
Molecular Function (MF)hydroxymethyl-, formyl- and related transferase activity1.19e-141.558e-15Highly InformativeDirect
Molecular Function (MF)oxo-acid-lyase activity9.393e-106.896e-10Highly InformativeDirect

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 7.575e-08 Least Informative Direct
Biological Process (BP) biosynthetic process 0.6972 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.2902 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.05707 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.1207 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.8604 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.003472 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.4328 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.005398 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.03915 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.1167 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.6222 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.6933 Moderately Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 6.508e-05 Informative Direct
Biological Process (BP) vitamin metabolic process 0.0002569 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 6.9e-07 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.0001813 Informative Direct
Biological Process (BP) carbohydrate catabolic process 1.708e-05 Informative Direct
Biological Process (BP) hexose metabolic process 0 Informative Direct
Biological Process (BP) cellular amide metabolic process 1.052e-05 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 2.103e-05 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0.9167 Informative Inherited
Biological Process (BP) lipid catabolic process 0.02673 Informative Inherited
Biological Process (BP) fatty acid metabolic process 0.3625 Informative Inherited
Biological Process (BP) energy derivation by oxidation of organic compounds 0.4103 Informative Inherited
Biological Process (BP) glycolysis 3.121e-07 Highly Informative Direct
Biological Process (BP) carbohydrate transport 4.303e-05 Highly Informative Direct
Biological Process (BP) aerobic respiration 1.798e-05 Highly Informative Direct
Biological Process (BP) cellular modified amino acid biosynthetic process 1.007e-09 Highly Informative Direct
Biological Process (BP) amide biosynthetic process 1.296e-08 Highly Informative Direct
Biological Process (BP) glyoxylate metabolic process 0 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.002967 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) cation binding 2.119e-06 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.001145 Moderately Informative Inherited
Molecular Function (MF) magnesium ion binding 0.0001014 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) kinase activity 0.4502 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.0707 Informative Inherited
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.0705 Informative Inherited
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 1.558e-15 Highly Informative Direct
Molecular Function (MF) oxo-acid-lyase activity 6.896e-10 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 1 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.002738 Least Informative Inherited
Cellular Component (CC) plastid 7.873e-05 Informative Direct
Cellular Component (CC) chloroplast stroma 1.924e-05 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)Lyases0Least InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0Least InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep0Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases1Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a nitrogenous group as ac0InformativeDirect
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0InformativeDirect
Enzyme Commission (EC)Oxo-acid-lyases2.387e-05InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases0.259InformativeInherited
Enzyme Commission (EC)Phosphoenolpyruvate--protein phosphotransferase0Highly InformativeDirect
Enzyme Commission (EC)Pyruvate kinase0Highly InformativeDirect
Enzyme Commission (EC)Pyruvate, phosphate dikinase8.653e-09Highly InformativeDirect
Enzyme Commission (EC)Pyruvate, water dikinase7.34e-07Highly InformativeDirect

Document: EC 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)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorous-containing groups1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-carbon lyases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0.7451InformativeInherited
Enzyme Commission (EC)Intramolecular transferases (mutases)1InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a nitrogenous group as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Phosphotransferases with paired acceptors0Highly InformativeDirect
Enzyme Commission (EC)Oxo-acid-lyases5.031e-07Highly InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases0.3579Highly InformativeInherited
Enzyme Commission (EC)Phosphotransferases (phosphomutases)1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processGlycolysis0InformativeDirect
Biological processTricarboxylic acid cycle0InformativeDirect
Biological processAromatic hydrocarbons catabolism1.737e-11InformativeDirect
Biological processPhosphotransferase system0Highly InformativeDirect
Biological processSugar transport0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPeroxisome0InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionPotassium0InformativeDirect
Molecular functionPyruvate0Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cofactor metabolism0Least InformativeDirect
UniPathway (UP)carbohydrate metabolism5.782e-11Least InformativeDirect
UniPathway (UP)aromatic compound metabolism1Least InformativeInherited
UniPathway (UP)lipid metabolism1Least InformativeInherited
UniPathway (UP)organic acid metabolism3.004e-12Moderately InformativeDirect
UniPathway (UP)fatty acid metabolism1.118e-06Moderately InformativeDirect
UniPathway (UP)carbohydrate degradation0.02343Moderately InformativeInherited
UniPathway (UP)energy metabolism0.1246Moderately InformativeInherited
UniPathway (UP)carbohydrate biosynthesis1Moderately InformativeInherited
UniPathway (UP)organic acid degradation4.523e-16InformativeDirect
UniPathway (UP)glycolysis2.868e-10InformativeDirect
UniPathway (UP)carbohydrate acid metabolism3.637e-10InformativeDirect
UniPathway (UP)gluconeogenesis0.0002157InformativeDirect
UniPathway (UP)(R)-pantothenate biosynthesis0Highly InformativeDirect
UniPathway (UP)4-hydroxyphenylacetate degradation0Highly InformativeDirect
UniPathway (UP)carbon fixation0Highly InformativeDirect
UniPathway (UP)aldaric acid degradation0Highly InformativeDirect
UniPathway (UP)propanoate metabolism2.19e-09Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR015813 SSF51621 Protein matches
Abstract

Pyruvate kinase controls the exit from the glysolysis pathway, catalysing the transfer of phosphate from phosphooenolpyruvate (PEP) to ADP. Mammalian pyruvate kinase is a homotetramer, where each polypeptide subunit consists of four domains: N-terminal, A domain, B domain and C-terminal. Activation of the enzyme is believed to occur via the clamping down of the B domain onto the A domain to dehydrate the active site cleft. The N- and C-terminal domains are situated at inter-subunit contact sites, and could be involved in assembly and communication within the complex. The N-terminal domain has a TIM beta/alpha-barrel structure. Homologous TIM-barrel domains are found in the following proteins:

  • N-terminal of pyruvate kinase , which is interrupted by an all-beta domain [PubMed11563914].
  • C-terminal of pyruvate phosphate dikinase , which has a similar mode of substrate binding to pyruvate kinase [PubMed11790099].
  • Phosphoenolpyruvate carboxylase ; this domain has additional helices [PubMed12467579].
  • Phosphenolpyruvate mutase/Isocitrate lyase , where it forms a swapped dimer [PubMed11526312].
  • HpcH/HpaI aldolases, such as the beta subunit of citrate lyase, where it forms a swapped dimer, and contains a pyruvate kinase-type metal binding site [PubMed7064730].
  • Ketopantoate hydroxymethyltransferase PanB , where a C-terminal helix exchange is observed in some enzymes [PubMed12906829].

InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · 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 24 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 Phosphoenolpyruvate/pyruvate domain 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 24 hidden Markov models representing the Phosphoenolpyruvate/pyruvate domain 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]