SUPERFAMILY 1.75 HMM library and genome assignments server

Nucleotide-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Nucleotide-binding domain [ 51970]
Superfamily:   Nucleotide-binding domain [ 51971] (3)
Families:   N-terminal domain of adrenodoxin reductase-like [ 51972] (5)
  D-aminoacid oxidase, N-terminal domain [ 51979]
  UDP-galactopyranose mutase, N-terminal domain [ 69427]


Superfamily statistics
Genomes (2,648) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 10,403 52,057 25
Proteins 8,765 43,370 21


Functional annotation
General category General
Detailed category Small molecule binding

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)nitrogen compound metabolic process0.000051450.0002837Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.00027940.000000000000001913Least InformativeDirect
Biological Process (BP)single-organism cellular process0.0021690.2822Least InformativeInherited
Biological Process (BP)response to stimulus0.00020831Least InformativeInherited
Biological Process (BP)multicellular organismal process0.000026281Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.000000081470.00000000009992Moderately InformativeDirect
Biological Process (BP)regulation of biological quality0.00000076380.6583Moderately InformativeInherited
Biological Process (BP)multi-organism process0.00000073110.7076Moderately InformativeInherited
Biological Process (BP)reproductive process0.000000036080.3329Moderately InformativeInherited
Biological Process (BP)multi-multicellular organism process0.000000000017850.00002336InformativeDirect
Biological Process (BP)single-organism behavior0.00000000008660.0005392InformativeDirect
Biological Process (BP)regulation of hormone levels0.00000000013720.00003626InformativeDirect
Biological Process (BP)sexual reproduction0.0000000014560.03098InformativeInherited
Biological Process (BP)multicellular organismal reproductive process0.0000000010410.02419InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process0.000000000028040.1021InformativeInherited

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) nitrogen compound metabolic process 0.0002837 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.000000000000001913 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.3021 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.2822 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.4627 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.9217 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.5098 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.00000000009992 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.000000007555 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.0003782 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0005284 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.001961 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.05592 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.01061 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.6583 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.9153 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.3953 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.7076 Moderately Informative Inherited
Biological Process (BP) reproductive process 0.3329 Moderately Informative Inherited
Biological Process (BP) multi-multicellular organism process 0.00002336 Informative Direct
Biological Process (BP) single-organism behavior 0.0005392 Informative Direct
Biological Process (BP) regulation of hormone levels 0.00003626 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.00369 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.004059 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.001603 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.9755 Informative Inherited
Biological Process (BP) sexual reproduction 0.03098 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.02419 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.1021 Informative Inherited
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.1105 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.000008087 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0098 Moderately Informative Inherited
Molecular Function (MF) cofactor binding 0 Informative Direct
Molecular Function (MF) nucleotide binding 0.000000636 Informative Direct
Molecular Function (MF) NADP binding 0.000000004752 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.000256 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) membrane 0.8538 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.2436 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.0008808 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.002665 Moderately Informative Inherited

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)Transferring one-carbon groups0.00166Least InformativeInherited
Enzyme Commission (EC)Methyltransferases0.00004935Moderately InformativeDirect
Enzyme Commission (EC)Acting on the CH-CH group of donors0.00005545Moderately InformativeDirect
Enzyme Commission (EC)Acting on a sulfur group of donors0.1189Moderately InformativeInherited
Enzyme Commission (EC)Acting on iron-sulfur proteins as donors0.00000000004213InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.0000002483InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0.000003472InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.09521InformativeInherited
Enzyme Commission (EC)Dihydropyrimidine dehydrogenase (NADP(+))0Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0Highly InformativeDirect
Enzyme Commission (EC)tRNA (5-methylaminomethyl-2-thiouridylate)-methylt0Highly InformativeDirect
Enzyme Commission (EC)Glutamate synthase (NADPH)0.0000002152Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect

Document: YP 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

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.003421Moderately InformativeInherited
Enzyme Commission (EC)Isomerases0.4636Moderately InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)Acting on the CH-NH(2) group of donors0InformativeDirect
Enzyme Commission (EC)Intramolecular transferases (mutases)0.003728InformativeInherited
Enzyme Commission (EC)Acting on a sulfur group of donors0.05197InformativeInherited
Enzyme Commission (EC)Acting on iron-sulfur proteins as donors0.000000000003851Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00000001023Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0.00000509Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.07851Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.09905Least InformativeInherited
Biological processLipid metabolism0.02125Moderately InformativeInherited
Biological processAmino-acid biosynthesis0.1856Moderately InformativeInherited
Biological processSteroid metabolism0.0000000004095InformativeDirect
Biological processElectron transport0.0000001404InformativeDirect
Biological processtRNA processing0.000001025InformativeDirect
Biological processCholesterol metabolism0.000000000564Highly InformativeDirect
Cellular componentPeroxisome0InformativeDirect
DomainTransit peptide0.00004549Moderately InformativeDirect
DomainRedox-active center0.00007197InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionIron0.0000000007835Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Molecular functionNADP0InformativeDirect
Molecular functionFAD0.0000000005626InformativeDirect
Molecular functionS-adenosyl-L-methionine0.0006979InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationMethyltransferase0.000001116InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0.00003085Least InformativeDirect
UniPathway (UP)lipid metabolism0.0001298Least InformativeDirect
UniPathway (UP)biopolymer metabolism0.4048Least InformativeInherited
UniPathway (UP)organic acid metabolism0.000000000003135Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism0.0000000103Moderately InformativeDirect
UniPathway (UP)biopolymer biosynthesis0.01378Moderately InformativeInherited
UniPathway (UP)glycan metabolism0.03827Moderately InformativeInherited
UniPathway (UP)cellular component biogenesis0.05707Moderately InformativeInherited
UniPathway (UP)membrane lipid metabolism0.5633Moderately InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis1Moderately InformativeInherited
UniPathway (UP)lipid biosynthesis1Moderately InformativeInherited
UniPathway (UP)L-glutamate metabolism0InformativeDirect
UniPathway (UP)organic acid biosynthesis0InformativeDirect
UniPathway (UP)terpene metabolism0.0000000000696InformativeDirect
UniPathway (UP)nonprotein amino-acid biosynthesis0.000000003606InformativeDirect
UniPathway (UP)lipopolysaccharide biosynthesis0.006447InformativeInherited
UniPathway (UP)beta-alanine biosynthesis0Highly InformativeDirect
UniPathway (UP)cholesterol metabolism0Highly InformativeDirect
UniPathway (UP)L-glutamate biosynthesis0Highly InformativeDirect
UniPathway (UP)LPS O-antigen biosynthesis0.0000001114Highly 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) · Yeast Phenotype (YP) · Fly Phenotype (FP) · 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 9 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 Nucleotide-binding domain 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 9 hidden Markov models representing the Nucleotide-binding domain 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) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]