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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 (2,649) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 10,401 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-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) organonitrogen compound metabolic process 0.0000000002777 Least Informative Direct
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.1326 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.405 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.4311 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.8381 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.721 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.01505 Least Informative Inherited
Biological Process (BP) organic substance catabolic process 0.0000001029 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0000001355 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.0000004671 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.00001423 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.0009491 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.4199 Moderately Informative Inherited
Biological Process (BP) glycosyl compound metabolic process 0.02641 Moderately Informative Inherited
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) dicarboxylic acid metabolic process 0.000001734 Informative Direct
Biological Process (BP) organonitrogen compound catabolic process 0.000002573 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.000002634 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0.000006596 Informative Direct
Biological Process (BP) glutamine family amino acid metabolic process 0.0001578 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.1244 Informative Inherited
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound catabolic process 0.0000000000001859 Highly Informative Direct
Biological Process (BP) dicarboxylic acid biosynthetic process 0.000000002411 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.0003364 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.00000004273 Moderately Informative Direct
Molecular Function (MF) anion binding 0.001856 Moderately Informative Inherited
Molecular Function (MF) coenzyme binding 0.2363 Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH2 group of donors 0.000000000000002458 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on iron-sulfur proteins as donors 0.0000000522 Highly Informative Direct
Molecular Function (MF) NADP binding 0.0000001086 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.00003415 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.09687 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least 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)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)retarded heterochronic variations0.4606Least InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.0002627Moderately InformativeDirect
Worm Phenotype (WP)body length variant0.00003311InformativeDirect
Worm Phenotype (WP)life span variant0.00006783InformativeDirect
Worm Phenotype (WP)brood size variant0.0001634InformativeDirect
Worm Phenotype (WP)hatching variant0.000000001409Highly InformativeDirect
Worm Phenotype (WP)extended life span0.000001021Highly InformativeDirect

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 groups0.002768Moderately InformativeInherited
Enzyme Commission (EC)Isomerases0.4472Moderately 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 transferases0.004109InformativeInherited
Enzyme Commission (EC)Acting on a sulfur group of donors0.04967InformativeInherited
Enzyme Commission (EC)Acting on iron-sulfur proteins as donors0.0000000000002225Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.000000008904Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0.0000143Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.1351Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.05849Least InformativeInherited
Biological processLipid metabolism0.02444Moderately InformativeInherited
Biological processAmino-acid biosynthesis0.1864Moderately InformativeInherited
Biological processSteroid metabolism0.0000000008246InformativeDirect
Biological processElectron transport0.00000001607InformativeDirect
Biological processtRNA processing0.000001047InformativeDirect
Biological processCholesterol metabolism0.00000000104Highly InformativeDirect
Cellular componentMitochondrion0.0003573Moderately InformativeDirect
Cellular componentPeroxisome0InformativeDirect
DomainTransit peptide0.00001199Moderately InformativeDirect
DomainRedox-active center0.00007671InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular functionIron0.000000001096Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Molecular functionNADP0InformativeDirect
Molecular functionFAD0.000000001298InformativeDirect
Molecular functionS-adenosyl-L-methionine0.0006564InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationMethyltransferase0.000001016InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0.00003092Least InformativeDirect
UniPathway (UP)lipid metabolism0.0001376Least InformativeDirect
UniPathway (UP)biopolymer metabolism0.4178Least InformativeInherited
UniPathway (UP)organic acid metabolism0.000000000006252Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism0.00000001115Moderately InformativeDirect
UniPathway (UP)biopolymer biosynthesis0.01433Moderately InformativeInherited
UniPathway (UP)glycan metabolism0.04026Moderately InformativeInherited
UniPathway (UP)cellular component biogenesis0.05779Moderately InformativeInherited
UniPathway (UP)membrane lipid metabolism0.5657Moderately 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)nonprotein amino-acid biosynthesis0.000000003935InformativeDirect
UniPathway (UP)steroid metabolism0.000000004053InformativeDirect
UniPathway (UP)lipopolysaccharide biosynthesis0.006528InformativeInherited
UniPathway (UP)beta-alanine biosynthesis0Highly InformativeDirect
UniPathway (UP)L-glutamate biosynthesis0Highly InformativeDirect
UniPathway (UP)LPS O-antigen biosynthesis0.0000001496Highly InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · 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-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 ]