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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 (3,211) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 16,301 95,682 43
Proteins 16,261 95,541 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)single-organism cellular process0.0000000000000031190Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)biosynthetic process11Least InformativeInherited
Biological Process (BP)primary metabolic process11Least InformativeInherited
Biological Process (BP)generation of precursor metabolites and energy00Moderately InformativeDirect
Biological Process (BP)oxidation-reduction process0.0000000000027120.000000000008036Moderately InformativeDirect
Biological Process (BP)nucleoside phosphate metabolic process0.0062290.003366Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process11Moderately InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.088410.004887Moderately InformativeInherited
Biological Process (BP)lipid metabolic process0.99720.808Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process11Moderately InformativeInherited
Biological Process (BP)cellular catabolic process11Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process10.9538Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.50230.05412Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.18420.05429Moderately InformativeInherited
Biological Process (BP)single-organism catabolic process11Moderately InformativeInherited
Biological Process (BP)cellular aldehyde metabolic process0.000088410.00000001995InformativeDirect
Biological Process (BP)dicarboxylic acid metabolic process0.000000095580.0000000006932InformativeDirect
Biological Process (BP)cellular lipid catabolic process0.000017310.00002331InformativeDirect
Biological Process (BP)cellular respiration0.00049750.0004082InformativeDirect
Biological Process (BP)nicotinamide nucleotide metabolic process0.0000020190.000001625InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process0.000027390.0005792InformativeDirect
Biological Process (BP)fatty acid metabolic process0.018040.03202InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process0.11520.05297InformativeInherited
Biological Process (BP)cellular carbohydrate metabolic process0.036490.04319InformativeInherited
Biological Process (BP)carboxylic acid catabolic process11InformativeInherited
Biological Process (BP)aerobic respiration00Highly InformativeDirect
Biological Process (BP)fatty acid catabolic process0.00000014090.00006502Highly InformativeDirect
Biological Process (BP)branched-chain amino acid metabolic process0.000014960.0002418Highly InformativeDirect
Biological Process (BP)lipid modification0.00000011410.00003106Highly InformativeDirect
Biological Process (BP)glyoxylate metabolic process0.000000009070.00000000001032Highly InformativeDirect
Biological Process (BP)citrate metabolic process11Highly InformativeInherited
Molecular Function (MF)binding0.17781Least InformativeInherited
Molecular Function (MF)oxidoreductase activity00Moderately InformativeDirect
Molecular Function (MF)metal ion binding0.00000000016380.00000000000001473Moderately InformativeDirect
Molecular Function (MF)magnesium ion binding0.00000000017850.00000000005684InformativeDirect
Molecular Function (MF)coenzyme binding0.000072670.0003451InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor00.001787Highly InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.0000025690.000003381Least InformativeDirect
Cellular Component (CC)cytoplasmic part00Least InformativeDirect
Cellular Component (CC)macromolecular complex11Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.89181Least InformativeInherited
Cellular Component (CC)mitochondrial part0.0076030.0004298Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.017880.2566Moderately InformativeInherited
Cellular Component (CC)microbody0.000011460.00000002InformativeDirect
Cellular Component (CC)oxidoreductase complex0.00056650.0002415InformativeDirect
Cellular Component (CC)plastid0.11280.05917InformativeInherited
Cellular Component (CC)chloroplast stroma0.00012380.0001275Highly 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) single-organism cellular process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
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) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.000000000008036 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.003366 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.004887 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.808 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.9538 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.05412 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.05429 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0.00000001995 Informative Direct
Biological Process (BP) dicarboxylic acid metabolic process 0.0000000006932 Informative Direct
Biological Process (BP) cellular lipid catabolic process 0.00002331 Informative Direct
Biological Process (BP) cellular respiration 0.0004082 Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 0.000001625 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0005792 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.03202 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.05297 Informative Inherited
Biological Process (BP) cellular carbohydrate metabolic process 0.04319 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 1 Informative Inherited
Biological Process (BP) aerobic respiration 0 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.00006502 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0.0002418 Highly Informative Direct
Biological Process (BP) lipid modification 0.00003106 Highly Informative Direct
Biological Process (BP) glyoxylate metabolic process 0.00000000001032 Highly Informative Direct
Biological Process (BP) citrate metabolic process 1 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0.00000000000001473 Moderately Informative Direct
Molecular Function (MF) magnesium ion binding 0.00000000005684 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.0008244 Informative Direct
Molecular Function (MF) coenzyme binding 0.0003451 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 0.001787 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.000003381 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) macromolecular complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.0004298 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.2566 Moderately Informative Inherited
Cellular Component (CC) microbody 0.00000002 Informative Direct
Cellular Component (CC) oxidoreductase complex 0.0002415 Informative Direct
Cellular Component (CC) plastid 0.05917 Informative Inherited
Cellular Component (CC) chloroplast stroma 0.0001275 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

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the integument0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the immune system0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of limbs0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the endocrine system0Moderately InformativeDirect
Phenotypic Abnormality (PA)Growth abnormality0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the vasculature0Moderately InformativeDirect
Phenotypic Abnormality (PA)Functional respiratory abnormality0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skin morphology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of central motor function0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormal genital system morphology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of movement0Moderately InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)lifespan0.0004979InformativeDirect

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)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)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)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)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0Least InformativeDirect
Xenopus ANatomical entity (XAN)brain0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)female genitalia0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0Moderately 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)intestine0InformativeDirect
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

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 peptide0.00000000004551Moderately InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionNADP0Moderately InformativeDirect
Molecular functionCobalt0InformativeDirect
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 metabolism4.598e-16Least InformativeDirect
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)organic acid metabolism0.1476Moderately InformativeInherited
UniPathway (UP)carbohydrate degradation1Moderately InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis1Moderately InformativeInherited
UniPathway (UP)phospholipid metabolism0InformativeDirect
UniPathway (UP)carbohydrate acid metabolism0.0008895InformativeDirect
UniPathway (UP)organic acid degradation0.4863InformativeInherited
UniPathway (UP)L-leucine biosynthesis0Highly InformativeDirect
UniPathway (UP)acetyl-CoA biosynthesis0Highly InformativeDirect
UniPathway (UP)aldaric acid degradation0.00002047Highly 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) · Disease Ontology (DO) · Human Phenotype (HP) · 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) · Disease Ontology (DO) · Human Phenotype (HP) · 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 ]