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 (2,647) 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 process4.837e-050.0002853Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.00010540Least InformativeDirect
Biological Process (BP)response to stimulus0.00021031Least InformativeInherited
Biological Process (BP)multicellular organismal process2.985e-051Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process8.556e-081.282e-10Moderately InformativeDirect
Biological Process (BP)reproduction8.208e-080.475Moderately InformativeInherited
Biological Process (BP)regulation of biological quality8.115e-070.673Moderately InformativeInherited
Biological Process (BP)multi-organism process2.592e-070.2848Moderately InformativeInherited
Biological Process (BP)regulation of hormone levels1.386e-103.654e-05InformativeDirect
Biological Process (BP)multi-multicellular organism process1.799e-112.296e-05InformativeDirect
Biological Process (BP)single-organism behavior2.852e-100.0005525InformativeDirect
Biological Process (BP)multicellular organismal reproductive process1.3e-090.02752InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process2.695e-110.09607InformativeInherited

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 0.0002853 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.459 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 0.9429 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.2974 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.5058 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 1.282e-10 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0005762 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.0002243 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.002068 Moderately Informative Inherited
Biological Process (BP) reproduction 0.475 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.673 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.8837 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.4126 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.2848 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.04738 Moderately Informative Inherited
Biological Process (BP) regulation of hormone levels 3.654e-05 Informative Direct
Biological Process (BP) multi-multicellular organism process 2.296e-05 Informative Direct
Biological Process (BP) single-organism behavior 0.0005525 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.004105 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.004614 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.9886 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.02752 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.09607 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.001989 Informative Inherited
Biological Process (BP) nucleobase metabolic process 1.938e-15 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) anion binding 0.009784 Moderately Informative Inherited
Molecular Function (MF) nucleotide binding 6.374e-07 Informative Direct
Molecular Function (MF) cofactor binding 0 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.000262 Highly Informative Direct
Molecular Function (MF) NADP binding 4.661e-09 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.2402 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 0.8547 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.0008895 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.002707 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 0.05478 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)Methyltransferases4.935e-05Moderately InformativeDirect
Enzyme Commission (EC)Acting on the CH-CH group of donors5.545e-05Moderately InformativeDirect
Enzyme Commission (EC)Acting on a sulfur group of donors0.1189Moderately InformativeInherited
Enzyme Commission (EC)Acting on iron-sulfur proteins as donors4.213e-11InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor2.483e-07InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor3.472e-06InformativeDirect
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)2.152e-07Highly 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 donors3.851e-12Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1.023e-08Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor5.09e-06Highly 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 metabolism4.095e-10InformativeDirect
Biological processElectron transport1.404e-07InformativeDirect
Biological processtRNA processing1.025e-06InformativeDirect
Biological processCholesterol metabolism5.64e-10Highly InformativeDirect
Cellular componentPeroxisome0InformativeDirect
DomainTransit peptide4.549e-05Moderately InformativeDirect
DomainRedox-active center7.197e-05InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionIron7.835e-10Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Molecular functionNADP0InformativeDirect
Molecular functionFAD5.626e-10InformativeDirect
Molecular functionS-adenosyl-L-methionine0.0006979InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationMethyltransferase1.116e-06InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism3.085e-05Least InformativeDirect
UniPathway (UP)lipid metabolism0.0001298Least InformativeDirect
UniPathway (UP)biopolymer metabolism0.4048Least InformativeInherited
UniPathway (UP)organic acid metabolism3.135e-12Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism1.03e-08Moderately 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 metabolism6.96e-11InformativeDirect
UniPathway (UP)nonprotein amino-acid biosynthesis3.606e-09InformativeDirect
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 biosynthesis1.114e-07Highly 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 ]