SUPERFAMILY 1.75 HMM library and genome assignments server

Acyl-CoA dehydrogenase NM domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   Acyl-CoA dehydrogenase NM domain-like [ 56644]
Superfamily:   Acyl-CoA dehydrogenase NM domain-like [ 56645] (2)
Families:   Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains [ 56646] (9)
  acyl-CoA oxidase N-terminal domains [ 75600] (2)


Superfamily statistics
Genomes (2,165) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 25,813 113,743 21
Proteins 25,458 112,812 21


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

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 process0.00070210Least InformativeDirect
Biological Process (BP)multicellular organismal process0.0002581Least InformativeInherited
Biological Process (BP)developmental process0.0001381Least InformativeInherited
Biological Process (BP)single-organism cellular process0.0027621Least InformativeInherited
Biological Process (BP)response to stimulus0.0012171Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.00037851Least InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process0.0000013110.00000000000008636Moderately InformativeDirect
Biological Process (BP)tissue development0.0000010010.9044Moderately InformativeInherited
Biological Process (BP)cell differentiation0.0000083771Moderately InformativeInherited
Biological Process (BP)organic hydroxy compound metabolic process0.00000022080.002533Moderately InformativeInherited
Biological Process (BP)response to abiotic stimulus0.0000024930.9315Moderately InformativeInherited
Biological Process (BP)organ development0.000010831Moderately InformativeInherited
Biological Process (BP)muscle structure development0.0000000050570.1374InformativeInherited
Biological Process (BP)muscle tissue development0.00000000085880.0272InformativeInherited
Biological Process (BP)cardiovascular system development0.000000032310.3127InformativeInherited
Biological Process (BP)amino-acid betaine metabolic process0.0000000000092310.000000000001592Highly InformativeDirect
Biological Process (BP)response to cold0.00000000066530.0007751Highly InformativeDirect
Biological Process (BP)cardiocyte differentiation0.0000000000084180.0001162Highly InformativeDirect
Biological Process (BP)cardiac muscle tissue development0.000000000032090.0003288Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.0033550.00003959Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.003290Least InformativeInherited

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) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.00000000000008636 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0 Moderately Informative Direct
Biological Process (BP) tissue development 0.9044 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.002533 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.9315 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.3573 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) fatty acid metabolic process 0 Informative Direct
Biological Process (BP) lipid catabolic process 0 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0 Informative Direct
Biological Process (BP) muscle structure development 0.1374 Informative Inherited
Biological Process (BP) muscle tissue development 0.0272 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.02551 Informative Inherited
Biological Process (BP) cardiovascular system development 0.3127 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 1 Informative Inherited
Biological Process (BP) amino-acid betaine metabolic process 0.000000000001592 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0.00000005856 Highly Informative Direct
Biological Process (BP) response to cold 0.0007751 Highly Informative Direct
Biological Process (BP) regulation of cellular ketone metabolic process 0.0004631 Highly Informative Direct
Biological Process (BP) lipid modification 0 Highly Informative Direct
Biological Process (BP) cardiocyte differentiation 0.0001162 Highly Informative Direct
Biological Process (BP) cardiac muscle tissue development 0.0003288 Highly Informative Direct
Biological Process (BP) icosanoid metabolic process 0.00701 Highly Informative Inherited
Biological Process (BP) unsaturated fatty acid metabolic process 1 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.001163 Moderately Informative Inherited
Molecular Function (MF) nucleotide binding 0.00002818 Informative Direct
Molecular Function (MF) cofactor binding 0.000000001381 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00003959 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.000002529 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.004682 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 0.00000001037 Informative Direct
Cellular Component (CC) external encapsulating structure 0.0003782 Informative Direct
Cellular Component (CC) microbody 0 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)Acting on the CH-CH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or red0.1185Moderately InformativeInherited
Enzyme Commission (EC)With other acceptors0InformativeDirect
Enzyme Commission (EC)With reduced flavin or flavoprotein as one donor, 0.000000000002343Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0.0000000003663Highly InformativeDirect
Enzyme Commission (EC)With a flavin as acceptor0.00000001767Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.03903Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdomen0.04004Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of muscle physiology0.0005702Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.005826Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the urinary system0.02267Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of carbohydrate metabolism/homeostasis0.04631Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.07869Moderately InformativeInherited
Phenotypic Abnormality (PA)Lethargy0.00000134InformativeDirect
Phenotypic Abnormality (PA)Hypoglycemia0.000007328InformativeDirect
Phenotypic Abnormality (PA)Hepatic steatosis0.00009894InformativeDirect
Phenotypic Abnormality (PA)Abnormality of carboxylic acid metabolism0.0001918InformativeDirect
Phenotypic Abnormality (PA)Muscular hypotonia0.0005094InformativeDirect
Phenotypic Abnormality (PA)Abnormality of urine homeostasis0.004139InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lipid metabolism0.02184InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cell physiology0.02915InformativeInherited
Phenotypic Abnormality (PA)Dicarboxylic aciduria0.000000007004Highly InformativeDirect
Phenotypic Abnormality (PA)Decreased plasma carnitine0.00000007307Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0Least InformativeDirect
Mammalian Phenotype (MP)liver/biliary system phenotype0.0001921Moderately InformativeDirect
Mammalian Phenotype (MP)renal/urinary system phenotype0.02664Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal circulating amino acid level0.0004321InformativeDirect
Mammalian Phenotype (MP)abnormal circulating glucose level0.007158InformativeInherited
Mammalian Phenotype (MP)abnormal urine homeostasis0.02412InformativeInherited
Mammalian Phenotype (MP)abnormal circulating carnitine level0.00000000000147Highly InformativeDirect
Mammalian Phenotype (MP)hepatic steatosis0.00000002268Highly InformativeDirect
Mammalian Phenotype (MP)aciduria0.0000006438Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least 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)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.003685Moderately InformativeInherited
Xenopus ANatomical entity (XAN)skeletal muscle0.00003564InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)pollen tube cell0.00002455InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage0.0003579Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)L mature pollen stage0.00007744InformativeDirect
Plant structure DEvelopment stage (PDE)M germinated pollen stage0.0002409InformativeDirect

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)Acting on paired donors, with incorporation or reduction of molecular oxygen0.0568InformativeInherited
Enzyme Commission (EC)Acting on CH or CH(2) groups0.5612InformativeInherited
Enzyme Commission (EC)With oxygen as acceptor0.000000000847Highly InformativeDirect
Enzyme Commission (EC)With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen0.000002776Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism0Moderately InformativeDirect
Biological processAromatic hydrocarbons catabolism0InformativeDirect
Biological processFatty acid metabolism0InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentPeroxisome0InformativeDirect
DiseaseDisease mutation0.0000008843Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionFAD0InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationS-nitrosylation0.000002859InformativeDirect

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)aromatic compound metabolism0.8995Least InformativeInherited
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)fatty acid metabolism0Moderately InformativeDirect
UniPathway (UP)amino-acid degradation0.000001464Moderately InformativeDirect
UniPathway (UP)amine and polyamine metabolism0.00007281Moderately InformativeDirect
UniPathway (UP)Branched-chain amino-acid degradation0InformativeDirect
UniPathway (UP)fatty acid degradation8.993e-16InformativeDirect
UniPathway (UP)carnitine metabolism0.00000000000003266InformativeDirect
UniPathway (UP)siderophore metabolism0.0000002252InformativeDirect
UniPathway (UP)4-hydroxyphenylacetate degradation0.0000000000001895Highly InformativeDirect
UniPathway (UP)fatty acid beta-oxidation1Highly InformativeInherited

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR009100 SSF56645 Protein matches
Abstract

Acyl-CoA dehydrogenases are a family of flavoproteins that catalyse the alpha,beta-dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with the concomitant reduction of enzyme-bound FAD. Different family members share a high sequence identity, catalytic mechanisms, and structural properties, but differ in the position of their catalytic bases and in their substrate binding specificity. Butyryl-CoA dehydrogenase [PubMed11812788] prefers short chain substrates, medium chain- and long-chain acyl-CoA dehydrogenases prefer medium and long chain substrates, respectively, and Isovaleryl-CoA dehydrogenase [PubMed9214289] prefers branched-chain substrates.

The monomeric enzyme is folded into three domains of approximately equal size, where the N-terminal domain is all-alpha, the middle domain is an open (5,8) barrel, and the C-terminal domain is a four-helical bundle. The constituent families differ in the numbers of C-terminal domains. This entry represents both the N-terminal and middle domains found in medium chain acyl-CoA dehydrogenases, as well as in the related peroxisomal acyl-CoA oxidase-II enzymes. Acyl-CoA oxidase (ACO) catalyzes the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids [PubMed11872165].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · 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 14 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 Acyl-CoA dehydrogenase NM domain-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 14 hidden Markov models representing the Acyl-CoA dehydrogenase NM domain-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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · 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 ]