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6-phosphogluconate dehydrogenase C-terminal domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   6-phosphogluconate dehydrogenase C-terminal domain-like [ 48178]
Superfamily:   6-phosphogluconate dehydrogenase C-terminal domain-like [ 48179] (12)
Families:   Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain [ 48180] (2)
  Mannitol 2-dehydrogenase [ 81843]
  Acetohydroxy acid isomeroreductase (ketol-acid reductoisomerase, KARI) [ 48184] (2)
  HCDH C-domain-like [ 48187] (2)
  Conserved hypothetical protein MTH1747 [ 74762]
  UDP-glucose/GDP-mannose dehydrogenase dimerisation domain [ 48191] (2)
  N-(1-D-carboxylethyl)-L-norvaline dehydrogenase [ 48194]
  Glycerol-3-phosphate dehydrogenase [ 48197]
  Ketopantoate reductase PanE [ 69084]
  ProC C-terminal domain-like [ 116984] (2)
  HMD dimerization domain-like [ 140777]
  TyrA dimerization domain-like [ 140780]


Superfamily statistics
Genomes (3,237) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 43,242 242,182 37
Proteins 39,073 217,639 36


Functional annotation
General category Metabolism
Detailed category Energy

Document:
Function annotation of SCOP domain superfamilies

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 0.000000000000003764 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.007857 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.0115 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.7281 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.6341 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.5326 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.00000000000003469 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.0000000000002801 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.000000007045 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.000000009348 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.0001221 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0007013 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.01214 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.185 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.9788 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.4627 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.5775 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.946 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.007302 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.007663 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.601 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.09515 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.1607 Moderately Informative Inherited
Biological Process (BP) nicotinamide nucleotide metabolic process 0 Informative Direct
Biological Process (BP) cellular aldehyde metabolic process 0 Informative Direct
Biological Process (BP) cellular lipid catabolic process 0.000000000005539 Informative Direct
Biological Process (BP) polysaccharide metabolic process 0.000000002206 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.000002367 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0.000008231 Informative Direct
Biological Process (BP) glutamine family amino acid metabolic process 0.0000362 Informative Direct
Biological Process (BP) response to oxidative stress 0.00009579 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0.0001216 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0005768 Informative Direct
Biological Process (BP) water-soluble vitamin biosynthetic process 0.0006542 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.0009112 Informative Direct
Biological Process (BP) alcohol metabolic process 0.9279 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 1 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 1 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.1679 Informative Inherited
Biological Process (BP) glucose 6-phosphate metabolic process 0 Highly Informative Direct
Biological Process (BP) glyceraldehyde-3-phosphate metabolic process 0 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.0000000000516 Highly Informative Direct
Biological Process (BP) NADP metabolic process 0.00000000007312 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0.0000003462 Highly Informative Direct
Biological Process (BP) cellular polysaccharide biosynthetic process 0.000004994 Highly Informative Direct
Biological Process (BP) lipid modification 0.00001435 Highly Informative Direct
Biological Process (BP) response to osmotic stress 0.00001437 Highly Informative Direct
Biological Process (BP) aromatic amino acid family biosynthetic process 0.00002176 Highly Informative Direct
Biological Process (BP) nucleotide-sugar metabolic process 0.0007464 Highly Informative Direct
Biological Process (BP) cellular response to abiotic stimulus 0.02635 Highly Informative Inherited
Biological Process (BP) polyol metabolic process 0.003398 Highly Informative Inherited
Biological Process (BP) cellular modified amino acid biosynthetic process 0.006023 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.0000003027 Moderately Informative Direct
Molecular Function (MF) anion binding 0.3008 Moderately Informative Inherited
Molecular Function (MF) isomerase activity 0.002686 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.007364 Moderately Informative Inherited
Molecular Function (MF) coenzyme binding 0 Informative Direct
Molecular Function (MF) hydro-lyase activity 0 Informative Direct
Molecular Function (MF) racemase and epimerase activity 0.00000009866 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.09336 Informative Inherited
Molecular Function (MF) NAD binding 0 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, transposing C=C bonds 0.00000000004752 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 0.000001446 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH group of donors 0.00009863 Highly Informative Direct
Molecular Function (MF) NADP binding 0.0002048 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.9662 Highly Informative Inherited
Cellular Component (CC) macromolecular complex 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.003327 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) microbody 0.000000001716 Informative Direct
Cellular Component (CC) protein-DNA complex 0.01164 Informative Inherited
Cellular Component (CC) chromosome 0.7445 Informative Inherited
Cellular Component (CC) chromatin 0.2488 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Isomerases0.00000000001634Least InformativeDirect
Enzyme Commission (EC)Lyases0.04828Least InformativeInherited
Enzyme Commission (EC)Racemases and epimerases0Moderately InformativeDirect
Enzyme Commission (EC)Hydro-lyases0Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0.00000000001304Moderately InformativeDirect
Enzyme Commission (EC)Acting on the CH-NH group of donors1Moderately InformativeInherited
Enzyme Commission (EC)Acting on the CH-CH group of donors1Moderately InformativeInherited
Enzyme Commission (EC)Transposing C==C bonds0InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)3-hydroxybutyryl-CoA epimerase0Highly InformativeDirect
Enzyme Commission (EC)3-hydroxyacyl-CoA dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)Dodecenoyl-CoA isomerase0Highly InformativeDirect
Enzyme Commission (EC)Enoyl-CoA hydratase0Highly InformativeDirect
Enzyme Commission (EC)Acting on hydrogen as donor0.003492Highly 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 digestive system0.1612Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.121Moderately InformativeInherited
Phenotypic Abnormality (PA)Hepatic steatosis0.0001925Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.0255Least InformativeInherited
Worm Phenotype (WP)lipid metabolism variant0.00002437InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)fertile0Moderately InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)tissue0.0604Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical cluster0.1395Least InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.0005318Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.01075Moderately InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.0003237InformativeDirect
Xenopus ANatomical entity (XAN)connective tissue0.0004935InformativeDirect
Xenopus ANatomical entity (XAN)duct0.0007431InformativeDirect
Xenopus ANatomical entity (XAN)solid compound organ0.002145InformativeInherited

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0.000514Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0.6306Least InformativeInherited
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0.0002938Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0.0003026Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0.0003722Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0.000636Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0.000689Least InformativeDirect

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)Lyases0.3075Least InformativeInherited
Enzyme Commission (EC)Acting on the CH-OH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.00000000001062Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)Racemases and epimerases0InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0.000000000007515InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.0003775InformativeDirect
Enzyme Commission (EC)Acting on the CH-NH group of donors1InformativeInherited
Enzyme Commission (EC)Intramolecular transferases1InformativeInherited
Enzyme Commission (EC)Transposing C=C bonds0Highly InformativeDirect
Enzyme Commission (EC)Acting on hydrogen as donors0.01676Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processLipid metabolism0Moderately InformativeDirect
Biological processLipid degradation0.0000001257InformativeDirect
Biological processBranched-chain amino acid biosynthesis0Highly InformativeDirect
Biological processPhospholipid metabolism0Highly InformativeDirect
Biological processMethanogenesis0.000000001856Highly InformativeDirect
Biological processAromatic amino acid biosynthesis1Highly InformativeInherited
Cellular componentCytoplasm0.0000002766Least InformativeDirect
Cellular componentPeroxisome0.000007117InformativeDirect
DiseaseCrown gall tumor0.0000008489InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionNADP0Moderately InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase0.000000000168Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0Least InformativeDirect
UniPathway (UP)lipid metabolism0Least InformativeDirect
UniPathway (UP)biopolymer metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)aromatic compound metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)membrane lipid metabolism0Moderately InformativeDirect
UniPathway (UP)fatty acid metabolism0.2577Moderately InformativeInherited
UniPathway (UP)organic acid metabolism0.9297Moderately InformativeInherited
UniPathway (UP)biopolymer biosynthesis1Moderately InformativeInherited
UniPathway (UP)carbohydrate degradation1Moderately InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis1Moderately InformativeInherited
UniPathway (UP)amino-acid degradation1Moderately InformativeInherited
UniPathway (UP)glycan metabolism1Moderately InformativeInherited
UniPathway (UP)one-carbon metabolism1Moderately InformativeInherited
UniPathway (UP)amine and polyamine metabolism1Moderately InformativeInherited
UniPathway (UP)nucleotide metabolism1Moderately InformativeInherited
UniPathway (UP)aromatic compound biosynthesis1Moderately InformativeInherited
UniPathway (UP)cellular component biogenesis1Moderately InformativeInherited
UniPathway (UP)L-isoleucine biosynthesis0InformativeDirect
UniPathway (UP)fatty acid degradation0InformativeDirect
UniPathway (UP)Branched-chain amino-acid degradation0.0000000000002255InformativeDirect
UniPathway (UP)carnitine metabolism0.0000000006183InformativeDirect
UniPathway (UP)methanogenesis0.00005571InformativeDirect
UniPathway (UP)nucleotide-sugar biosynthesis0.0003941InformativeDirect
UniPathway (UP)phospholipid metabolism1InformativeInherited
UniPathway (UP)glycolipid biosynthesis1InformativeInherited
UniPathway (UP)aromatic amino-acid biosynthesis1InformativeInherited
UniPathway (UP)UDP-alpha-D-glucuronate biosynthesis0Highly InformativeDirect
UniPathway (UP)L-valine biosynthesis0Highly InformativeDirect
UniPathway (UP)pentose phosphate pathway0Highly InformativeDirect
UniPathway (UP)L-tyrosine biosynthesis0Highly InformativeDirect
UniPathway (UP)glycerophospholipid metabolism0Highly InformativeDirect
UniPathway (UP)pentose and glucuronate interconversion0.00000000000001075Highly InformativeDirect
UniPathway (UP)methanogenesis from CO(2)0.000000005426Highly InformativeDirect
UniPathway (UP)alginate biosynthesis0.000001858Highly InformativeDirect
UniPathway (UP)butanoate metabolism0.0001366Highly InformativeDirect
UniPathway (UP)L-proline biosynthesis0.0001498Highly InformativeDirect
UniPathway (UP)prephenate biosynthesis0.0002446Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR008927 SSF48179 Protein matches
Abstract

6-phosphogluconate dehydrogenase catalyses the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate with the concomitant reduction of NADP to NADPH. The metazoan 6PGDHs have a well-conserved glycine-serine rich sequence at the C-terminus, which is lacking from bacterial enzymes and from those of the parasitic protozoan Trypanosoma brucei. The active dimer of the mammalian enzyme assembles with the C-terminal tail of one subunit threaded through the other, forming part of the substrate-binding site. The tail of T. brucei 6PGDH is shorter than that of the mammalian enzyme and its terminal residues associate tightly with the second monomer. The three-dimensional structure shows this generates additional interactions between the subunits close to the active site; the coenzyme-binding domain is thereby associated more tightly with the helical domain. Three residues, conserved in all other known sequences, are important in creating a salt bridge between monomers close to the substrate-binding site [PubMed9737929].

This domain is structurally similar to domains found in several different families, including those represented by mannitol 2-dehydrogenase, acetohydroxy acid isomeroreductase, short chain L-3-hydroxyacyl CoA dehydrogenase, UDP-glucose/GDP-mannose dehydrogenase (dimerisation domain), N-(1-D-carboxylethyl)-L-norvaline dehydrogenase, glycerol-3-phosphate dehydrogenase, and ketopantoate reductase (PanE).


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-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · 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 26 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 6-phosphogluconate dehydrogenase C-terminal domain-like 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 26 hidden Markov models representing the 6-phosphogluconate dehydrogenase C-terminal domain-like 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-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]