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 (3,163) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 16,088 42,127 43
Proteins 16,049 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 process0.60940.6546Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.23120.6182Least InformativeInherited
Biological Process (BP)response to stimulus0.79421Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process3.685e-083.886e-12Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process11Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.84560.8665Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process11Moderately InformativeInherited
Biological Process (BP)cellular catabolic process11Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.032420.001396Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.08360.01382Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.0014625.038e-05Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.1230.03443Moderately InformativeInherited
Biological Process (BP)cellular lipid metabolic process0.91220.6544Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process11Moderately InformativeInherited
Biological Process (BP)response to oxidative stress0.00085810.0001507InformativeDirect
Biological Process (BP)energy derivation by oxidation of organic compounds1.35e-052.835e-06InformativeDirect
Biological Process (BP)lipid catabolic process5.414e-054.991e-05InformativeDirect
Biological Process (BP)cellular amide metabolic process6.78e-059.634e-06InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process3.307e-065.922e-07InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process1.888e-050.000334InformativeDirect
Biological Process (BP)fatty acid metabolic process0.031740.03691InformativeInherited
Biological Process (BP)cellular modified amino acid metabolic process0.88710.6664InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process0.2340.1548InformativeInherited
Biological Process (BP)carboxylic acid catabolic process11InformativeInherited
Biological Process (BP)glutathione metabolic process1.876e-075.73e-06Highly InformativeDirect
Biological Process (BP)aerobic respiration00Highly InformativeDirect
Biological Process (BP)fatty acid catabolic process5.093e-070.0001865Highly InformativeDirect
Biological Process (BP)branched-chain amino acid metabolic process5.241e-074.756e-06Highly InformativeDirect
Biological Process (BP)lipid modification3.022e-060.0001737Highly InformativeDirect
Biological Process (BP)nicotinamide nucleotide metabolic process1.53e-084.359e-08Highly InformativeDirect
Biological Process (BP)glutamate metabolic process0.86150.7795Highly InformativeInherited
Molecular Function (MF)binding0.2861Least InformativeInherited
Molecular Function (MF)oxidoreductase activity00Moderately InformativeDirect
Molecular Function (MF)cation binding1.182e-113.054e-15Moderately InformativeDirect
Molecular Function (MF)magnesium ion binding1.672e-093.243e-11InformativeDirect
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 acceptor00.0001452Highly InformativeDirect
Cellular Component (CC)cytoplasmic part1.211e-063.612e-12Least InformativeDirect
Cellular Component (CC)protein complex0.1610.6626Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.48620.9263Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.099030.1525Least InformativeInherited
Cellular Component (CC)cytoskeleton0.039410.126Moderately InformativeInherited
Cellular Component (CC)mitochondrial part0.002520.0001452Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.013370.2625Moderately InformativeInherited
Cellular Component (CC)mitochondrial matrix1.248e-092.233e-10InformativeDirect
Cellular Component (CC)plastid0.13490.08828InformativeInherited
Cellular Component (CC)microtubule cytoskeleton0.00094880.007421InformativeInherited
Cellular Component (CC)lipid particle0.00046940.0005019Highly InformativeDirect
Cellular Component (CC)microtubule associated complex2.059e-061.545e-06Highly InformativeDirect
Cellular Component (CC)chloroplast stroma2.877e-054.201e-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 0.6546 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.6182 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 3.886e-12 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 5.038e-05 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.8665 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 0.001396 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.01382 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.03443 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.6544 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) response to oxidative stress 0.0001507 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 2.835e-06 Informative Direct
Biological Process (BP) lipid catabolic process 4.991e-05 Informative Direct
Biological Process (BP) cellular amide metabolic process 9.634e-06 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 5.922e-07 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.000334 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.03691 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.6664 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.1548 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 1 Informative Inherited
Biological Process (BP) glutathione metabolic process 5.73e-06 Highly Informative Direct
Biological Process (BP) aerobic respiration 0 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.0001865 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 4.756e-06 Highly Informative Direct
Biological Process (BP) lipid modification 0.0001737 Highly Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 4.359e-08 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.7795 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 3.054e-15 Moderately Informative Direct
Molecular Function (MF) magnesium ion binding 3.243e-11 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 0.0001452 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 3.612e-12 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.1525 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.9263 Least Informative Inherited
Cellular Component (CC) protein complex 0.6626 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.0001452 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.126 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.2625 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 2.233e-10 Informative Direct
Cellular Component (CC) microbody 0.0002453 Informative Direct
Cellular Component (CC) plastid 0.08828 Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.007421 Informative Inherited
Cellular Component (CC) lipid particle 0.0005019 Highly Informative Direct
Cellular Component (CC) microtubule associated complex 1.545e-06 Highly Informative Direct
Cellular Component (CC) chloroplast stroma 4.201e-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)fertile0Least InformativeDirect
Fly Phenotype (FP)increased mortality0Least 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 peptide3.738e-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) 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 ]