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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 (2,653) 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) organonitrogen compound metabolic process 0.01298 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.001563 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.4818 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.1595 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.4145 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.4432 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.5923 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.00000009867 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0000001882 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0000009354 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.00003714 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0172 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.3274 Moderately Informative Inherited
Biological Process (BP) dicarboxylic acid metabolic process 0.0000001815 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.000002754 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0.00000656 Informative Direct
Biological Process (BP) glycosyl compound metabolic process 0.0000324 Informative Direct
Biological Process (BP) glutamine family amino acid metabolic process 0.00006013 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.07685 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 0.00000000002156 Highly Informative Direct
Biological Process (BP) dicarboxylic acid biosynthetic process 0.0000000001337 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.0001017 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 0.000000271 Moderately Informative Direct
Molecular Function (MF) anion binding 0.001758 Moderately Informative Inherited
Molecular Function (MF) coenzyme binding 0.2741 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 0.00000004475 Highly Informative Direct
Molecular Function (MF) NADP binding 0.00000008144 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.0000321 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.05846 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.9798 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.06804Least InformativeInherited
Biological processLipid metabolism0.02669Moderately InformativeInherited
Biological processAmino-acid biosynthesis0.1107Moderately InformativeInherited
Biological processSteroid metabolism0.000000001092InformativeDirect
Biological processElectron transport0.00000001958InformativeDirect
Biological processtRNA processing0.000001261InformativeDirect
Biological processCholesterol metabolism0.000000001453Highly InformativeDirect
Cellular componentMitochondrion0.0004361Moderately InformativeDirect
Cellular componentPeroxisome0InformativeDirect
DomainTransit peptide0.0000082Moderately InformativeDirect
DomainRedox-active center0.00008651InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular functionNADP0Moderately InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionIron-sulfur0Moderately InformativeDirect
Molecular functionIron0.00000001476Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionFAD0.0000000001334InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationMethyltransferase0.000001271InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

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) · UniProtKB KeyWords (KW) · Internal database links ]