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  Home > SCOP hierarchy > Isocitrate/Isopropylmalate dehydrogenase-like superfamily


Isocitrate/Isopropylmalate dehydrogenase-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Isocitrate/Isopropylmalate dehydrogenase-like [ 53658]
Superfamily:   Isocitrate/Isopropylmalate dehydrogenase-like [ 53659] (5)
Families:   Dimeric isocitrate & isopropylmalate dehydrogenases [ 53660] (3)
  PdxA-like [ 102656]
  PlsX-like [ 102660]
  Phosphotransacetylase [ 102663] (2)
  Monomeric isocitrate dehydrogenase [ 82526]

 Superfamily statistics
Genomes (2,453) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 12,976 42,127 43
Proteins 12,939 42,086 43

 Functional annotation
General category Metabolism
Detailed category Redox

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 process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)biosynthetic process0.31070.3207Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.13120.4029Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process1.075e-073.209e-11Moderately InformativeDirect
Biological Process (BP)oxidation-reduction process5.301e-057.184e-05Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.00053142.731e-05Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process11Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.64060.5334Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process11Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.018140.0007504Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.49990.3316Moderately InformativeInherited
Biological Process (BP)energy derivation by oxidation of organic compounds1.527e-053.893e-06InformativeDirect
Biological Process (BP)cellular amide metabolic process6.672e-058.628e-06InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process2.269e-064.665e-07InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process1.093e-050.0002496InformativeDirect
Biological Process (BP)oxidoreduction coenzyme metabolic process0.0027490.03736InformativeInherited
Biological Process (BP)cellular modified amino acid metabolic process0.67730.4723InformativeInherited
Biological Process (BP)glutamine family amino acid metabolic process0.15550.09742InformativeInherited
Biological Process (BP)glutathione metabolic process1.601e-078.049e-06Highly InformativeDirect
Biological Process (BP)aerobic respiration00Highly InformativeDirect
Biological Process (BP)branched-chain amino acid metabolic process2.22e-050.0001293Highly InformativeDirect
Biological Process (BP)dicarboxylic acid metabolic process9.249e-124.032e-14Highly InformativeDirect
Biological Process (BP)nicotinamide nucleotide metabolic process3.092e-085.356e-08Highly InformativeDirect
Biological Process (BP)glutamine family amino acid biosynthetic process0.0013470.005641Highly InformativeInherited
Molecular Function (MF)binding0.40481Least InformativeInherited
Molecular Function (MF)oxidoreductase activity00Moderately InformativeDirect
Molecular Function (MF)cation binding5.184e-111.038e-14Moderately InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on CH-OH group of donors00InformativeDirect
Molecular Function (MF)magnesium ion binding3.393e-091.187e-10Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor00.0001376Highly InformativeDirect
Cellular Component (CC)cytoplasmic part2.337e-086.149e-15Least InformativeDirect
Cellular Component (CC)protein complex0.087270.5053Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle0.96581Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.33890.7478Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.086290.1488Least InformativeInherited
Cellular Component (CC)cytoskeleton0.6260.4369Moderately InformativeInherited
Cellular Component (CC)mitochondrial part0.012320.0004413Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.0011220.111Moderately InformativeInherited
Cellular Component (CC)plastid0.2240.1419InformativeInherited
Cellular Component (CC)microtubule cytoskeleton0.002610.01231InformativeInherited
Cellular Component (CC)microtubule associated complex6.887e-062.652e-06Highly InformativeDirect
Cellular Component (CC)chloroplast stroma5.116e-056.894e-05Highly 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 0 Least Informative Direct
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) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.3207 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.4029 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 3.209e-11 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.0007504 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 7.184e-05 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 2.731e-05 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.5334 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 1 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.3316 Moderately Informative Inherited
Biological Process (BP) response to oxidative stress 0.0006906 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 3.893e-06 Informative Direct
Biological Process (BP) cellular amide metabolic process 8.628e-06 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 4.665e-07 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0002496 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.03736 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.4723 Informative Inherited
Biological Process (BP) glutamine family amino acid metabolic process 0.09742 Informative Inherited
Biological Process (BP) glutathione metabolic process 8.049e-06 Highly Informative Direct
Biological Process (BP) aerobic respiration 0 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0.0001293 Highly Informative Direct
Biological Process (BP) dicarboxylic acid metabolic process 4.032e-14 Highly Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 5.356e-08 Highly Informative Direct
Biological Process (BP) glutamine family amino acid biosynthetic process 0.005641 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) cation binding 1.038e-14 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on CH-OH group of donors 0 Informative Direct
Molecular Function (MF) magnesium ion binding 1.187e-10 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 0.0001376 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 6.149e-15 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.7478 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1488 Least Informative Inherited
Cellular Component (CC) protein complex 0.5053 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.0004413 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.4369 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.111 Moderately Informative Inherited
Cellular Component (CC) plastid 0.1419 Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.01231 Informative Inherited
Cellular Component (CC) microtubule associated complex 2.652e-06 Highly Informative Direct
Cellular Component (CC) chloroplast stroma 6.894e-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)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases1Moderately InformativeInherited
Enzyme Commission (EC)Phosphate acetyltransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)development0InformativeDirect

Document: YP 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)lethal0Least InformativeDirect
Fly Phenotype (FP)fertile0Least InformativeDirect

Document: FP 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)male genitalia0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)intestine0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)immune system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)skin0InformativeDirect
Xenopus ANatomical entity (XAN)heart0InformativeDirect
Xenopus ANatomical entity (XAN)spleen0InformativeDirect
Xenopus ANatomical entity (XAN)tail0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least 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)Lyases1Least InformativeInherited
Enzyme Commission (EC)Acting on the CH-OH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-carbon lyases1Moderately InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)Carboxy-lyases1InformativeInherited

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 biosynthesis0InformativeDirect
Biological processTricarboxylic acid cycle0InformativeDirect
Biological processBranched-chain amino acid biosynthesis0Highly InformativeDirect
Biological processPhospholipid biosynthesis0Highly InformativeDirect
Biological processPyridoxine biosynthesis0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DomainTransit peptide1.594e-11Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0.0009802Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionCobalt0InformativeDirect
Molecular functionNADP0InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)lipid metabolism0Least InformativeDirect
UniPathway (UP)amino-acid metabolism3.302e-15Least InformativeDirect
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)organic acid metabolism0.07033Moderately InformativeInherited
UniPathway (UP)carbohydrate degradation1Moderately InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis1Moderately InformativeInherited
UniPathway (UP)phospholipid metabolism0InformativeDirect
UniPathway (UP)organic acid degradation0.5897InformativeInherited
UniPathway (UP)L-leucine biosynthesis0Highly InformativeDirect
UniPathway (UP)acetyl-CoA biosynthesis0Highly InformativeDirect
UniPathway (UP)aldaric acid degradation1.935e-05Highly InformativeDirect

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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · 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 22 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 Isocitrate/Isopropylmalate dehydrogenase-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 22 hidden Markov models representing the Isocitrate/Isopropylmalate dehydrogenase-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 · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.