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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 (2,647) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 10,392 52,057 25
Proteins 8,755 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 process0.000047390.0002839Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.00010460Least InformativeDirect
Biological Process (BP)response to stimulus0.00020741Least InformativeInherited
Biological Process (BP)multicellular organismal process0.000029621Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.000000087870.0000000001463Moderately InformativeDirect
Biological Process (BP)reproduction0.000000081670.4727Moderately InformativeInherited
Biological Process (BP)regulation of biological quality0.00000077820.6624Moderately InformativeInherited
Biological Process (BP)multi-organism process0.0000002490.275Moderately InformativeInherited
Biological Process (BP)multi-multicellular organism process0.000000000017610.00002261InformativeDirect
Biological Process (BP)regulation of hormone levels0.00000000013880.00003625InformativeDirect
Biological Process (BP)single-organism behavior0.00000000026570.0005262InformativeDirect
Biological Process (BP)multicellular organismal reproductive process0.0000000013020.02699InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process0.000000000027010.09648InformativeInherited

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 0.0002839 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.4586 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) biosynthetic process 0.9415 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.2969 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.5051 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.0000000001463 Moderately Informative Direct
Biological Process (BP) organic cyclic compound catabolic process 0.000005798 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.0002175 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.000572 Moderately Informative Direct
Biological Process (BP) reproduction 0.4727 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.6624 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.8604 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.4091 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.275 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.002007 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.04676 Moderately Informative Inherited
Biological Process (BP) multi-multicellular organism process 0.00002261 Informative Direct
Biological Process (BP) regulation of hormone levels 0.00003625 Informative Direct
Biological Process (BP) single-organism behavior 0.0005262 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.004106 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.004627 Informative Inherited
Biological Process (BP) glycosyl compound catabolic process 0.002956 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.9892 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.02699 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.09648 Informative Inherited
Biological Process (BP) pyrimidine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0.000000000000001931 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.1134 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 0.01571 Moderately Informative Inherited
Molecular Function (MF) cofactor binding 0 Informative Direct
Molecular Function (MF) nucleotide binding 0.00000427 Informative Direct
Molecular Function (MF) NADP binding 0.000000001013 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.0001951 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.3206 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) membrane 0.8473 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.0008926 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.002692 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 0.05389 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 groups0.003479Moderately InformativeInherited
Enzyme Commission (EC)Isomerases0.4642Moderately 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)0.003706InformativeInherited
Enzyme Commission (EC)Acting on a sulfur group of donors0.05327InformativeInherited
Enzyme Commission (EC)Acting on iron-sulfur proteins as donors0.000000000004164Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00000001034Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0.000005Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.08026Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.09897Least InformativeInherited
Biological processLipid metabolism0.02135Moderately InformativeInherited
Biological processAmino-acid biosynthesis0.1862Moderately InformativeInherited
Biological processSteroid metabolism0.0000000004177InformativeDirect
Biological processElectron transport0.0000001419InformativeDirect
Biological processtRNA processing0.0000009856InformativeDirect
Biological processCholesterol metabolism0.0000000005665Highly InformativeDirect
Cellular componentPeroxisome0InformativeDirect
DomainTransit peptide0.00004494Moderately InformativeDirect
DomainRedox-active center0.00007274InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionIron0.0000000008124Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Molecular functionNADP0InformativeDirect
Molecular functionFAD0.0000000005836InformativeDirect
Molecular functionS-adenosyl-L-methionine0.0007126InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationMethyltransferase0.000001118InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0.001901Least InformativeInherited
UniPathway (UP)nonprotein amino-acid biosynthesis0.000000000000003273InformativeDirect
UniPathway (UP)steroid metabolism0.000000002165InformativeDirect
UniPathway (UP)cholesterol metabolism0Highly 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 ]