SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 (2,653) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 10,423 62,707 25
Proteins 8,785 52,058 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) single-organism cellular process 0.0006393 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.1618 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.4882 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.01249 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.452 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.5917 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.4219 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.0000001017 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0000002184 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.000001008 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.00004357 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.01632 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.3295 Moderately Informative Inherited
Biological Process (BP) dicarboxylic acid metabolic process 0.0000002094 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.000002927 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0.000007111 Informative Direct
Biological Process (BP) glycosyl compound metabolic process 0.00003289 Informative Direct
Biological Process (BP) glutamine family amino acid metabolic process 0.00005824 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.07578 Informative Inherited
Biological Process (BP) pyrimidine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) nucleoside catabolic process 0.00000000002663 Highly Informative Direct
Biological Process (BP) dicarboxylic acid biosynthetic process 0.0000000001461 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.0001082 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 0.0000001422 Moderately Informative Direct
Molecular Function (MF) anion binding 0.001941 Moderately Informative Inherited
Molecular Function (MF) coenzyme binding 0.2634 Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH2 group of donors 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on iron-sulfur proteins as donors 0.00000005198 Highly Informative Direct
Molecular Function (MF) NADP binding 0.00000008525 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.00003757 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.1565 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 variations0.4604Least InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.0002697Moderately InformativeDirect
Worm Phenotype (WP)body length variant0.00003421InformativeDirect
Worm Phenotype (WP)life span variant0.0000883InformativeDirect
Worm Phenotype (WP)brood size variant0.0001797InformativeDirect
Worm Phenotype (WP)hatching variant0.000000001681Highly InformativeDirect
Worm Phenotype (WP)extended life span0.000001205Highly 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 groups0.002819Moderately InformativeInherited
Enzyme Commission (EC)Isomerases0.4469Moderately 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 transferases0.004249InformativeInherited
Enzyme Commission (EC)Acting on a sulfur group of donors0.05386InformativeInherited
Enzyme Commission (EC)Acting on iron-sulfur proteins as donors0.000000000000271Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00000000996Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0.00004454Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.08097Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.06278Least InformativeInherited
Biological processLipid metabolism0.02547Moderately InformativeInherited
Biological processAmino-acid biosynthesis0.1067Moderately InformativeInherited
Biological processSteroid metabolism0.000000000951InformativeDirect
Biological processElectron transport0.00000001775InformativeDirect
Biological processtRNA processing0.000001154InformativeDirect
Biological processCholesterol metabolism0.000000001233Highly InformativeDirect
Cellular componentMitochondrion0.0003977Moderately InformativeDirect
Cellular componentPeroxisome0InformativeDirect
DomainTransit peptide0.000008096Moderately InformativeDirect
DomainRedox-active center0.00007719InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionIron-sulfur0Moderately InformativeDirect
Molecular functionNADP0Moderately InformativeDirect
Molecular functionIron0.00000004311Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionFAD0.0000000001217InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationMethyltransferase0.000001114InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0.0000136Least InformativeDirect
UniPathway (UP)lipid metabolism0.0000555Least InformativeDirect
UniPathway (UP)biopolymer metabolism0.4777Least InformativeInherited
UniPathway (UP)organic acid metabolism0.000000000000271Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism0.0000000009526Moderately InformativeDirect
UniPathway (UP)biopolymer biosynthesis0.01836Moderately InformativeInherited
UniPathway (UP)glycan metabolism0.04481Moderately InformativeInherited
UniPathway (UP)cellular component biogenesis0.07378Moderately InformativeInherited
UniPathway (UP)membrane lipid metabolism0.6771Moderately 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 biosynthesis0.000000008478InformativeDirect
UniPathway (UP)steroid metabolism0.00000001169InformativeDirect
UniPathway (UP)lipopolysaccharide biosynthesis0.00839InformativeInherited
UniPathway (UP)beta-alanine biosynthesis0Highly InformativeDirect
UniPathway (UP)L-glutamate biosynthesis0Highly InformativeDirect
UniPathway (UP)LPS O-antigen biosynthesis0.0000001488Highly 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 ]