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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 (3,233) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 43,158 242,182 37
Proteins 38,997 217,639 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) organonitrogen compound metabolic process 0.0000000000000208 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000000003622 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.02527 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.6087 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 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) heterocycle metabolic process 0.7061 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.01549 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00000000000002413 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.0000000006171 Moderately Informative Direct
Biological Process (BP) ribose phosphate metabolic process 0.00000002904 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.0000001793 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.0001935 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0004889 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.02753 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.6414 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.9493 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.5223 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.03006 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.5445 Moderately Informative Inherited
Biological Process (BP) response to stress 0.762 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.008476 Moderately Informative Inherited
Biological Process (BP) pyridine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) cellular aldehyde metabolic process 0 Informative Direct
Biological Process (BP) lipid catabolic process 0.00000000003274 Informative Direct
Biological Process (BP) polysaccharide metabolic process 0.000000001312 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.00000007441 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.0000005861 Informative Direct
Biological Process (BP) glutamine family amino acid metabolic process 0.00004222 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0.00005603 Informative Direct
Biological Process (BP) response to oxidative stress 0.00007169 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0.0001676 Informative Direct
Biological Process (BP) water-soluble vitamin biosynthetic process 0.0004739 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.0008793 Informative Direct
Biological Process (BP) alcohol metabolic process 0.9009 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.1861 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 1 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 1 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 1 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.001614 Informative Inherited
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) fatty acid catabolic process 0.000000000001946 Highly Informative Direct
Biological Process (BP) NADP metabolic process 0.0000000002204 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0.0000002504 Highly Informative Direct
Biological Process (BP) cellular polysaccharide biosynthetic process 0.000003822 Highly Informative Direct
Biological Process (BP) lipid modification 0.00003899 Highly Informative Direct
Biological Process (BP) aromatic amino acid family biosynthetic process 0.0001103 Highly Informative Direct
Biological Process (BP) nucleotide-sugar metabolic process 0.0005449 Highly Informative Direct
Biological Process (BP) internal protein amino acid acetylation 0.0006499 Highly Informative Direct
Biological Process (BP) cellular response to abiotic stimulus 0.0226 Highly Informative Inherited
Biological Process (BP) cellular modified amino acid biosynthetic process 0.009819 Highly Informative Inherited
Biological Process (BP) polyol metabolic process 0.003441 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 0.0000005051 Moderately Informative Direct
Molecular Function (MF) anion binding 0.4669 Moderately Informative Inherited
Molecular Function (MF) protein binding 1 Moderately Informative Inherited
Molecular Function (MF) isomerase activity 0.002479 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.0126 Moderately Informative Inherited
Molecular Function (MF) hydro-lyase activity 0 Informative Direct
Molecular Function (MF) coenzyme binding 0 Informative Direct
Molecular Function (MF) racemase and epimerase activity 0.0000001 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.0894 Informative Inherited
Molecular Function (MF) NAD binding 0.00000000000005571 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, transposing C=C bonds 0.00000000004869 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 0.000001485 Highly Informative Direct
Molecular Function (MF) NADP binding 0.0000197 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH group of donors 0.00006678 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 1 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.0001097 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) microbody 0.0000000008628 Informative Direct

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 system0.06268Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.1314Moderately InformativeInherited
Phenotypic Abnormality (PA)Hepatic steatosis0.00008042Highly 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 variant0.02102Least InformativeInherited
Worm Phenotype (WP)fat content variant0.000001455InformativeDirect

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)tissue0.05864Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical cluster0.1407Least InformativeInherited
Xenopus ANatomical entity (XAN)musculoskeletal system0.0005167Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0.01037Moderately InformativeInherited
Xenopus ANatomical entity (XAN)skeletal system0.0003127InformativeDirect
Xenopus ANatomical entity (XAN)connective tissue0.0005109InformativeDirect
Xenopus ANatomical entity (XAN)duct0.0007406InformativeDirect
Xenopus ANatomical entity (XAN)solid compound organ0.002148InformativeInherited

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)Lyases0.2808Least InformativeInherited
Enzyme Commission (EC)Acting on the CH-OH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.00000000002649Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)Racemases and epimerases0InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0.00000000001247InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.0004412InformativeDirect
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 donors0.01713Highly 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 degradation0.0000001212InformativeDirect
Biological processBranched-chain amino acid biosynthesis0Highly InformativeDirect
Biological processPhospholipid metabolism0Highly InformativeDirect
Biological processMethanogenesis0.000000001873Highly InformativeDirect
Biological processAromatic amino acid biosynthesis1Highly InformativeInherited
Cellular componentCytoplasm0.0000001432Least InformativeDirect
Cellular componentPeroxisome0.000006254InformativeDirect
DiseaseCrown gall tumor0.0000008395InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionNADP0InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase0.000000002991Moderately 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 metabolism0.2652Moderately InformativeInherited
UniPathway (UP)organic acid metabolism0.9158Moderately 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 degradation0.0000000000002872InformativeDirect
UniPathway (UP)carnitine metabolism0.0000000006425InformativeDirect
UniPathway (UP)methanogenesis0.00005721InformativeDirect
UniPathway (UP)nucleotide-sugar biosynthesis0.0004151InformativeDirect
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 interconversion0.0000000000000116Highly InformativeDirect
UniPathway (UP)methanogenesis from CO(2)0.000000005581Highly InformativeDirect
UniPathway (UP)alginate biosynthesis0.00000189Highly InformativeDirect
UniPathway (UP)butanoate metabolism0.0001394Highly InformativeDirect
UniPathway (UP)L-proline biosynthesis0.0001587Highly InformativeDirect
UniPathway (UP)prephenate biosynthesis0.0002476Highly 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 ]