SUPERFAMILY 1.75 HMM library and genome assignments server

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 (3,205) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 16,267 92,048 43
Proteins 16,227 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)single-organism cellular process0.000000000000053510.000000000004614Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)biosynthetic process0.73370.764Least InformativeInherited
Biological Process (BP)response to stimulus0.76541Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.36850.7419Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.00000010360.00000000002009Moderately InformativeDirect
Biological Process (BP)oxidation-reduction process0.000000020520.00000000002278Moderately InformativeDirect
Biological Process (BP)small molecule biosynthetic process0.37230.1189Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.84580.5786Moderately InformativeInherited
Biological Process (BP)lipid metabolic process0.95520.7838Moderately InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process11Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.91280.9123Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.0028250.0001127Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process11Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.1960.03635Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.05950.002113Moderately InformativeInherited
Biological Process (BP)cellular catabolic process11Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process11Moderately InformativeInherited
Biological Process (BP)single-organism catabolic process11Moderately InformativeInherited
Biological Process (BP)response to oxidative stress0.0004910.00006835InformativeDirect
Biological Process (BP)energy derivation by oxidation of organic compounds00InformativeDirect
Biological Process (BP)lipid catabolic process0.000082870.00005782InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process0.0000049750.0000005447InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process0.000044990.0006286InformativeDirect
Biological Process (BP)fatty acid metabolic process0.078610.089InformativeInherited
Biological Process (BP)oxidoreduction coenzyme metabolic process0.0014680.0266InformativeInherited
Biological Process (BP)peptide metabolic process0.0016220.01262InformativeInherited
Biological Process (BP)cellular modified amino acid metabolic process0.83970.6012InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process0.22050.1319InformativeInherited
Biological Process (BP)carboxylic acid catabolic process11InformativeInherited
Biological Process (BP)glutathione metabolic process0.00000015680.000006265Highly InformativeDirect
Biological Process (BP)aerobic respiration00Highly InformativeDirect
Biological Process (BP)fatty acid catabolic process0.00000073350.0001592Highly InformativeDirect
Biological Process (BP)branched-chain amino acid metabolic process0.00000042540.0000035Highly InformativeDirect
Biological Process (BP)lipid modification0.0000026020.0001691Highly InformativeDirect
Biological Process (BP)nicotinamide nucleotide metabolic process0.000000030540.00000007469Highly InformativeDirect
Biological Process (BP)glutamate metabolic process0.93920.8859Highly InformativeInherited
Molecular Function (MF)binding0.34191Least InformativeInherited
Molecular Function (MF)oxidoreductase activity00Moderately InformativeDirect
Molecular Function (MF)cation binding0.000000000016830.000000000000006187Moderately InformativeDirect
Molecular Function (MF)magnesium ion binding0.0000000012640.00000000014InformativeDirect
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 acceptor00.00009763Highly InformativeDirect
Cellular Component (CC)cytoplasmic part0.000000016560.00000000000001325Least InformativeDirect
Cellular Component (CC)protein complex0.14990.6592Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.39950.8587Least InformativeInherited
Cellular Component (CC)non-membrane-bounded organelle0.54851Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.010010.02275Least InformativeInherited
Cellular Component (CC)mitochondrial part0.0059070.000337Moderately InformativeInherited
Cellular Component (CC)cytoskeleton0.88550.8301Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.0022810.06141Moderately InformativeInherited
Cellular Component (CC)mitochondrial matrix0.000000048180.00000001734InformativeDirect
Cellular Component (CC)lipid particle0.00020810.00001354InformativeDirect
Cellular Component (CC)oxidoreductase complex0.00020250.00007869InformativeDirect
Cellular Component (CC)plastid0.18480.1104InformativeInherited
Cellular Component (CC)microtubule cytoskeleton0.0025150.01704InformativeInherited
Cellular Component (CC)microtubule associated complex0.0000040420.000003212Highly InformativeDirect
Cellular Component (CC)chloroplast stroma0.000037070.0000554Highly 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 0.000000000004614 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.764 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.7419 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.00000000002009 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.00000000002278 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.0001127 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.1189 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.5786 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.7838 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.9123 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.03635 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.002113 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 1 Moderately Informative Inherited
Biological Process (BP) response to oxidative stress 0.00006835 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 0 Informative Direct
Biological Process (BP) lipid catabolic process 0.00005782 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0.0000005447 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0006286 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.089 Informative Inherited
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.0266 Informative Inherited
Biological Process (BP) peptide metabolic process 0.01262 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.6012 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.1319 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 1 Informative Inherited
Biological Process (BP) glutathione metabolic process 0.000006265 Highly Informative Direct
Biological Process (BP) aerobic respiration 0 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.0001592 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0.0000035 Highly Informative Direct
Biological Process (BP) lipid modification 0.0001691 Highly Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 0.00000007469 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.8859 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 0.000000000000006187 Moderately Informative Direct
Molecular Function (MF) magnesium ion binding 0.00000000014 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 0.00009763 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.00000000000001325 Least Informative Direct
Cellular Component (CC) protein complex 0.6592 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.02275 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.8587 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.000337 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.8301 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.06141 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 0.00000001734 Informative Direct
Cellular Component (CC) lipid particle 0.00001354 Informative Direct
Cellular Component (CC) microbody 0.0004561 Informative Direct
Cellular Component (CC) oxidoreductase complex 0.00007869 Informative Direct
Cellular Component (CC) plastid 0.1104 Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.01704 Informative Inherited
Cellular Component (CC) microtubule associated complex 0.000003212 Highly Informative Direct
Cellular Component (CC) chloroplast stroma 0.0000554 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 peptide0.00000000005258Moderately 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

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)lipid metabolism0Least InformativeDirect
UniPathway (UP)amino-acid metabolism8.993e-16Least InformativeDirect
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)organic acid metabolism0.09605Moderately InformativeInherited
UniPathway (UP)carbohydrate degradation1Moderately InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis1Moderately InformativeInherited
UniPathway (UP)phospholipid metabolism0InformativeDirect
UniPathway (UP)carbohydrate acid metabolism0.0008999InformativeDirect
UniPathway (UP)organic acid degradation0.5452InformativeInherited
UniPathway (UP)L-leucine biosynthesis0Highly InformativeDirect
UniPathway (UP)acetyl-CoA biosynthesis0Highly InformativeDirect
UniPathway (UP)aldaric acid degradation0.0000215Highly 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) · 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) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]