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 (2,641) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 10,355 0 25
Proteins 8,724 0 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 process3.985e-050.0001549Least InformativeDirect
Biological Process (BP)single-organism metabolic process8.611e-050Least InformativeDirect
Biological Process (BP)response to stimulus0.00017851Least InformativeInherited
Biological Process (BP)multicellular organismal process2.699e-051Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process7.112e-081.207e-10Moderately InformativeDirect
Biological Process (BP)reproduction7.2e-080.4533Moderately InformativeInherited
Biological Process (BP)multi-organism process1.836e-070.2409Moderately InformativeInherited
Biological Process (BP)regulation of hormone levels1.321e-103.38e-05InformativeDirect
Biological Process (BP)single-organism behavior2.227e-100.000424InformativeDirect
Biological Process (BP)multicellular organismal reproductive process1.185e-090.02514InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process2.154e-110.09255InformativeInherited

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 0.0001549 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.461 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 0.9056 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.2971 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.5086 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 1.207e-10 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0005561 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.0002102 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.001994 Moderately Informative Inherited
Biological Process (BP) reproduction 0.4533 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.8229 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.3916 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.2409 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.04605 Moderately Informative Inherited
Biological Process (BP) regulation of hormone levels 3.38e-05 Informative Direct
Biological Process (BP) single-organism behavior 0.000424 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.004309 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.004791 Informative Inherited
Biological Process (BP) glycosyl compound catabolic process 0.003133 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.9731 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.02514 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.09255 Informative Inherited
Biological Process (BP) nucleobase metabolic process 1.922e-15 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.121 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 0.0274 Moderately Informative Inherited
Molecular Function (MF) nucleotide binding 2.394e-05 Informative Direct
Molecular Function (MF) cofactor binding 6.048e-15 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.0001685 Highly Informative Direct
Molecular Function (MF) NADP binding 7.923e-09 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.4802 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 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.0008238 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.002531 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 0.05154 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 groups0.002209Moderately InformativeInherited
Enzyme Commission (EC)Isomerases0.6035Moderately 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)0.012InformativeInherited
Enzyme Commission (EC)Acting on a sulfur group of donors0.0426InformativeInherited
Enzyme Commission (EC)Acting on iron-sulfur proteins as donors3.052e-11Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor7.402e-09Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor4.148e-06Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.1206Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.07602Least InformativeInherited
Biological processLipid metabolism0.01714Moderately InformativeInherited
Biological processAmino-acid biosynthesis0.2737Moderately InformativeInherited
Biological processSteroid metabolism2.896e-10InformativeDirect
Biological processElectron transport8.791e-08InformativeDirect
Biological processtRNA processing5.877e-07InformativeDirect
Biological processCholesterol metabolism4.382e-10Highly InformativeDirect
Cellular componentPeroxisome0InformativeDirect
DomainTransit peptide4.57e-05Moderately InformativeDirect
DomainRedox-active center7.222e-05InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionIron1.199e-09Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Molecular functionNADP0InformativeDirect
Molecular functionFAD1.489e-09InformativeDirect
Molecular functionS-adenosyl-L-methionine0.000454InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationMethyltransferase6.572e-07InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)lipid metabolism6.093e-05Least InformativeDirect
UniPathway (UP)amino-acid metabolism7.035e-05Least InformativeDirect
UniPathway (UP)biopolymer metabolism0.3469Least InformativeInherited
UniPathway (UP)organic acid metabolism8.523e-11Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism5.857e-09Moderately InformativeDirect
UniPathway (UP)biopolymer biosynthesis0.01059Moderately InformativeInherited
UniPathway (UP)glycan metabolism0.03406Moderately InformativeInherited
UniPathway (UP)cellular component biogenesis0.1229Moderately InformativeInherited
UniPathway (UP)membrane lipid metabolism0.567Moderately InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis1Moderately InformativeInherited
UniPathway (UP)lipid biosynthesis1Moderately InformativeInherited
UniPathway (UP)L-glutamate metabolism2.274e-16InformativeDirect
UniPathway (UP)organic acid biosynthesis4.523e-16InformativeDirect
UniPathway (UP)terpene metabolism3.75e-11InformativeDirect
UniPathway (UP)nonprotein amino-acid biosynthesis1.508e-09InformativeDirect
UniPathway (UP)lipopolysaccharide biosynthesis0.004893InformativeInherited
UniPathway (UP)beta-alanine biosynthesis0Highly InformativeDirect
UniPathway (UP)cholesterol metabolism0Highly InformativeDirect
UniPathway (UP)L-glutamate biosynthesis0Highly InformativeDirect
UniPathway (UP)LPS O-antigen biosynthesis1.117e-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 ]