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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 (2,655) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 10,462 81,715 25
Proteins 8,813 67,670 21


Functional annotation
General category General
Detailed category Small molecule binding

Document:
Function annotation of SCOP domain superfamilies

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)developmental timing variant0.4241Least InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.0003162Moderately InformativeDirect
Worm Phenotype (WP)body region morphology variant0.0003219Moderately InformativeDirect
Worm Phenotype (WP)brood size variant0.00023InformativeDirect
Worm Phenotype (WP)life span variant0.001224InformativeInherited
Worm Phenotype (WP)hatching variant0.000000001912Highly InformativeDirect
Worm Phenotype (WP)extended life span0.000006916Highly InformativeDirect
Worm Phenotype (WP)reduced brood size0.0001393Highly 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 groups0.004961Moderately InformativeInherited
Enzyme Commission (EC)Isomerases0.4575Moderately 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 transferases0.004255InformativeInherited
Enzyme Commission (EC)Acting on a sulfur group of donors0.07501InformativeInherited
Enzyme Commission (EC)Acting on iron-sulfur proteins as donors0.0000000000006803Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00000001011Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0.00004562Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.08761Highly InformativeInherited

Document: EC annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Enzyme Commission (EC) ]

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 · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Enzyme Commission (EC) · Internal database links ]