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 (3,198) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 16,216 92,048 43
Proteins 16,177 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 process0.72090.7612Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.29980.7008Least InformativeInherited
Biological Process (BP)response to stimulus0.84851Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process1.097e-071.914e-11Moderately InformativeDirect
Biological Process (BP)oxidation-reduction process4.287e-062.266e-07Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process11Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.84720.8683Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process11Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process11Moderately InformativeInherited
Biological Process (BP)cellular catabolic process11Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.032640.001295Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.12620.02405Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.002690.0001087Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.11680.03218Moderately InformativeInherited
Biological Process (BP)cellular lipid metabolic process0.90870.6426Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process11Moderately InformativeInherited
Biological Process (BP)response to oxidative stress0.00051027.372e-05InformativeDirect
Biological Process (BP)energy derivation by oxidation of organic compounds1.667e-053.092e-06InformativeDirect
Biological Process (BP)lipid catabolic process0.00011376.74e-05InformativeDirect
Biological Process (BP)cellular amide metabolic process6.488e-052.129e-05InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process2.83e-064.651e-07InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process4.155e-050.0006165InformativeDirect
Biological Process (BP)oxidoreduction coenzyme metabolic process0.0030720.03905InformativeInherited
Biological Process (BP)fatty acid metabolic process0.030010.03759InformativeInherited
Biological Process (BP)cellular modified amino acid metabolic process0.85240.6113InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process0.19730.1201InformativeInherited
Biological Process (BP)carboxylic acid catabolic process11InformativeInherited
Biological Process (BP)glutathione metabolic process1.861e-075.088e-06Highly InformativeDirect
Biological Process (BP)aerobic respiration00Highly InformativeDirect
Biological Process (BP)fatty acid catabolic process1.1e-060.00017Highly InformativeDirect
Biological Process (BP)branched-chain amino acid metabolic process3.545e-072.807e-06Highly InformativeDirect
Biological Process (BP)lipid modification3.027e-060.0001692Highly InformativeDirect
Biological Process (BP)nicotinamide nucleotide metabolic process4.279e-089.465e-08Highly InformativeDirect
Biological Process (BP)glutamate metabolic process0.95430.9084Highly InformativeInherited
Molecular Function (MF)binding0.61351Least InformativeInherited
Molecular Function (MF)oxidoreductase activity00Moderately InformativeDirect
Molecular Function (MF)cation binding1.718e-106.626e-14Moderately InformativeDirect
Molecular Function (MF)magnesium ion binding1.39e-091.576e-10InformativeDirect
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 acceptor00.0001377Highly InformativeDirect
Cellular Component (CC)cytoplasmic part7.276e-093.132e-15Least InformativeDirect
Cellular Component (CC)protein complex0.31170.8656Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.43230.945Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.026770.06335Least InformativeInherited
Cellular Component (CC)cytoskeleton0.51060.3604Moderately InformativeInherited
Cellular Component (CC)mitochondrial part0.0065580.0003507Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.0035990.1396Moderately InformativeInherited
Cellular Component (CC)mitochondrial matrix3.659e-085.645e-09InformativeDirect
Cellular Component (CC)plastid0.18430.1072InformativeInherited
Cellular Component (CC)microtubule cytoskeleton0.0037040.02037InformativeInherited
Cellular Component (CC)microtubule associated complex6.661e-064.821e-06Highly InformativeDirect
Cellular Component (CC)chloroplast stroma5.15e-056.903e-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 0.7612 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.7008 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 1.914e-11 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 2.266e-07 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.0001087 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.8683 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 1 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) cofactor metabolic process 0.001295 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.02405 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.03218 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.6426 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) response to oxidative stress 7.372e-05 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 3.092e-06 Informative Direct
Biological Process (BP) lipid catabolic process 6.74e-05 Informative Direct
Biological Process (BP) cellular amide metabolic process 2.129e-05 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 4.651e-07 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0006165 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.03905 Informative Inherited
Biological Process (BP) fatty acid metabolic process 0.03759 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.6113 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.1201 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 1 Informative Inherited
Biological Process (BP) glutathione metabolic process 5.088e-06 Highly Informative Direct
Biological Process (BP) aerobic respiration 0 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.00017 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 2.807e-06 Highly Informative Direct
Biological Process (BP) lipid modification 0.0001692 Highly Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 9.465e-08 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.9084 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 6.626e-14 Moderately Informative Direct
Molecular Function (MF) magnesium ion binding 1.576e-10 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 0.0001377 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 3.132e-15 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.06335 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.945 Least Informative Inherited
Cellular Component (CC) protein complex 0.8656 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.0003507 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.3604 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.1396 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 5.645e-09 Informative Direct
Cellular Component (CC) microbody 0.0004397 Informative Direct
Cellular Component (CC) plastid 0.1072 Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.02037 Informative Inherited
Cellular Component (CC) microtubule associated complex 4.821e-06 Highly Informative Direct
Cellular Component (CC) chloroplast stroma 6.903e-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

Disease Ontology (DO)

(show details) Document: DO 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 peptide4.993e-11Moderately 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 metabolism6.77e-16Least InformativeDirect
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)organic acid metabolism0.09503Moderately InformativeInherited
UniPathway (UP)carbohydrate degradation1Moderately InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis1Moderately InformativeInherited
UniPathway (UP)phospholipid metabolism0InformativeDirect
UniPathway (UP)carbohydrate acid metabolism0.0009023InformativeDirect
UniPathway (UP)organic acid degradation0.5518InformativeInherited
UniPathway (UP)L-leucine biosynthesis0Highly InformativeDirect
UniPathway (UP)acetyl-CoA biosynthesis0Highly InformativeDirect
UniPathway (UP)aldaric acid degradation2.158e-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) · Disease Ontology (DO) · 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) · Disease Ontology (DO) · 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 ]