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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 (3,204) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 16,259 92,048 43
Proteins 16,219 92,004 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 process0.76780.7996Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.34750.7412Least InformativeInherited
Biological Process (BP)response to stimulus0.76071Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.00000019590.00000000003492Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process11Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.8770.8862Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process11Moderately InformativeInherited
Biological Process (BP)cellular catabolic process11Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.043910.001694Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.15260.03048Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.0030690.0001296Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.13890.03756Moderately InformativeInherited
Biological Process (BP)cellular lipid metabolic process0.92020.6727Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process11Moderately InformativeInherited
Biological Process (BP)response to oxidative stress0.00048160.00006324InformativeDirect
Biological Process (BP)energy derivation by oxidation of organic compounds0.0000058720.000001377InformativeDirect
Biological Process (BP)lipid catabolic process0.000084230.0000572InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process0.0000030330.0000004826InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process0.000057920.0007637InformativeDirect
Biological Process (BP)oxidoreduction coenzyme metabolic process0.0025950.03584InformativeInherited
Biological Process (BP)fatty acid metabolic process0.049310.05821InformativeInherited
Biological Process (BP)peptide metabolic process0.0010210.008146InformativeInherited
Biological Process (BP)cellular modified amino acid metabolic process0.86250.6198InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process0.20520.125InformativeInherited
Biological Process (BP)carboxylic acid catabolic process11InformativeInherited
Biological Process (BP)glutathione metabolic process0.00000024660.000005156Highly InformativeDirect
Biological Process (BP)aerobic respiration00Highly InformativeDirect
Biological Process (BP)fatty acid catabolic process0.00000074550.0001579Highly InformativeDirect
Biological Process (BP)branched-chain amino acid metabolic process0.00000037650.000003185Highly InformativeDirect
Biological Process (BP)lipid modification0.0000026540.0001668Highly InformativeDirect
Biological Process (BP)nicotinamide nucleotide metabolic process0.0000000330.00000007792Highly InformativeDirect
Biological Process (BP)glutamate metabolic process0.94030.8918Highly InformativeInherited
Molecular Function (MF)binding0.32681Least InformativeInherited
Molecular Function (MF)oxidoreductase activity00Moderately InformativeDirect
Molecular Function (MF)cation binding0.000000000016580.000000000000006038Moderately InformativeDirect
Molecular Function (MF)magnesium ion binding0.0000000012420.0000000001335InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on CH-OH group of donors00InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor00.0001019Highly InformativeDirect
Cellular Component (CC)cytoplasmic part0.000000013310.000000000000006075Least InformativeDirect
Cellular Component (CC)protein complex0.24240.8076Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.39290.8981Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.024910.05646Least InformativeInherited
Cellular Component (CC)cytoskeleton0.51370.3679Moderately InformativeInherited
Cellular Component (CC)mitochondrial part0.0055790.0003033Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.0034930.131Moderately InformativeInherited
Cellular Component (CC)mitochondrial matrix0.000000037530.000000006792InformativeDirect
Cellular Component (CC)plastid0.17570.104InformativeInherited
Cellular Component (CC)microtubule cytoskeleton0.0025180.01634InformativeInherited
Cellular Component (CC)microtubule associated complex0.000004310.000003448Highly InformativeDirect
Cellular Component (CC)chloroplast stroma0.000037690.00005581Highly 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 0.7996 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.7412 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.00000000003492 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.0001296 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.8862 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.001694 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.03048 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.03756 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.6727 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) response to oxidative stress 0.00006324 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 0.000001377 Informative Direct
Biological Process (BP) lipid catabolic process 0.0000572 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0.0000004826 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0007637 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.03584 Informative Inherited
Biological Process (BP) fatty acid metabolic process 0.05821 Informative Inherited
Biological Process (BP) peptide metabolic process 0.008146 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.6198 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.125 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 1 Informative Inherited
Biological Process (BP) glutathione metabolic process 0.000005156 Highly Informative Direct
Biological Process (BP) aerobic respiration 0 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.0001579 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0.000003185 Highly Informative Direct
Biological Process (BP) lipid modification 0.0001668 Highly Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 0.00000007792 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.8918 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 0.000000000000006038 Moderately Informative Direct
Molecular Function (MF) magnesium ion binding 0.0000000001335 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on CH-OH group of donors 0 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 0.0001019 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.000000000000006075 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.05646 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.8981 Least Informative Inherited
Cellular Component (CC) protein complex 0.8076 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.0003033 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.3679 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.131 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 0.000000006792 Informative Direct
Cellular Component (CC) microbody 0.0004122 Informative Direct
Cellular Component (CC) plastid 0.104 Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.01634 Informative Inherited
Cellular Component (CC) microtubule associated complex 0.000003448 Highly Informative Direct
Cellular Component (CC) chloroplast stroma 0.00005581 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

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)increased mortality0Least InformativeDirect
Fly Phenotype (FP)fertile0Moderately 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)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least 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) 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 metabolism0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DomainTransit peptide0.00000000004878Moderately InformativeDirect
Molecular functionMetal-binding0Least 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

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

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) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]