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Nucleotidylyl transferase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Adenine nucleotide alpha hydrolase-like [ 52373] (3)
Superfamily:   Nucleotidylyl transferase [ 52374] (5)
Families:   Class I aminoacyl-tRNA synthetases (RS), catalytic domain [ 52375] (12)
  Cytidylyltransferase [ 52394]
  Adenylyltransferase [ 52397] (5)
  Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC) [ 63976]
  ATP sulfurylase catalytic domain [ 63979]


Superfamily statistics
Genomes (3,259) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 58,787 315,428 81
Proteins 57,902 312,946 81


Functional annotation
General category Metabolism
Detailed category Nucleotide metabolism and transport

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)biosynthetic process0.00000000000017460Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.00000000000041450Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.00000000000074070Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.00000000036890Least InformativeDirect
Biological Process (BP)single-organism cellular process0.0000000025310Least InformativeDirect
Biological Process (BP)cellular aromatic compound metabolic process0.0000063550Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.0000069030Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.000031770Least InformativeDirect
Biological Process (BP)primary metabolic process0.24590.0002761Least InformativeInherited
Biological Process (BP)macromolecule metabolic process0.99530.0005994Least InformativeInherited
Biological Process (BP)cofactor metabolic process0.0000000000000016250.00008355Moderately InformativeDirect
Biological Process (BP)RNA metabolic process0.000000020760Moderately InformativeDirect
Biological Process (BP)organophosphate biosynthetic process0.00000038550.0001828Moderately InformativeDirect
Biological Process (BP)nucleoside phosphate metabolic process0.00000066160.00000234Moderately InformativeDirect
Biological Process (BP)gene expression0.000039870Moderately InformativeDirect
Biological Process (BP)cellular amino acid metabolic process0.00018450Moderately InformativeDirect
Biological Process (BP)lipid metabolic process0.95630.7755Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.023431Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.036561Moderately InformativeInherited
Biological Process (BP)amide biosynthetic process0.0053070Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process0.66331Moderately InformativeInherited
Biological Process (BP)purine-containing compound metabolic process0.0056520.2004Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.12440.9815Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.0037941Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.94331Moderately InformativeInherited
Biological Process (BP)peptide metabolic process0.0015370Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.058450Moderately InformativeInherited
Biological Process (BP)tRNA metabolic process00InformativeDirect
Biological Process (BP)water-soluble vitamin biosynthetic process0.00000000011350.00000003575InformativeDirect
Biological Process (BP)coenzyme biosynthetic process0.00000000052710.0000000000001202InformativeDirect
Biological Process (BP)monocarboxylic acid biosynthetic process0.0000000089580.0004399InformativeDirect
Biological Process (BP)nucleotide biosynthetic process0.000001530.000000000125InformativeDirect
Biological Process (BP)glycerolipid metabolic process0.00097870.0000005566InformativeDirect
Biological Process (BP)phospholipid metabolic process0.2660.00000008018InformativeInherited
Biological Process (BP)purine-containing compound biosynthetic process0.034070.5894InformativeInherited
Biological Process (BP)pyridine-containing compound metabolic process0.000022330.01591InformativeInherited
Biological Process (BP)cellular modified amino acid metabolic process0.00000039950.03465InformativeInherited
Biological Process (BP)oxidoreduction coenzyme metabolic process0.70281InformativeInherited
Biological Process (BP)ammonium ion metabolic process0.069640.00154InformativeInherited
Biological Process (BP)NAD metabolic process00.000000000000505Highly InformativeDirect
Biological Process (BP)ribonucleoside bisphosphate biosynthetic process0.0000000000019810Highly InformativeDirect
Biological Process (BP)purine nucleoside bisphosphate biosynthetic process0.0000000000019810Highly InformativeDirect
Biological Process (BP)pyridine-containing compound biosynthetic process0.0000053730.000498Highly InformativeDirect
Biological Process (BP)glycerophospholipid biosynthetic process0.000064740.0000000166Highly InformativeDirect
Biological Process (BP)phosphatidylcholine metabolic process0.00015790.00000009783Highly InformativeDirect
Biological Process (BP)coenzyme A metabolic process0.00017680.0000007781Highly InformativeDirect
Biological Process (BP)cellular modified amino acid biosynthetic process0.000017790.2529Highly InformativeInherited
Molecular Function (MF)binding0.98041Least InformativeInherited
Molecular Function (MF)transferase activity0.00068291Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups00Moderately InformativeDirect
Molecular Function (MF)small molecule binding0.023380.07415Moderately InformativeInherited
Molecular Function (MF)anion binding0.026490.1525Moderately InformativeInherited
Molecular Function (MF)carbohydrate derivative binding0.0036660.006445Moderately InformativeInherited
Molecular Function (MF)ligase activity00InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity00InformativeDirect
Molecular Function (MF)purine ribonucleoside triphosphate binding0.00028470.00002475InformativeDirect
Molecular Function (MF)purine nucleotide binding0.00063550.00014InformativeDirect
Molecular Function (MF)ribonucleotide binding0.00093320.0001858InformativeDirect
Molecular Function (MF)acid-amino acid ligase activity00.0004851Highly InformativeDirect
Molecular Function (MF)ATP binding0.0000018480.0000002194Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.021270.02184Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.69850.0000002208Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.31761Moderately InformativeInherited

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) biosynthetic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0002761 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0005994 Least Informative Direct
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cofactor metabolic process 0.00008355 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0.0001828 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.00000234 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) peptide metabolic process 0 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.5027 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.7755 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) purine-containing compound metabolic process 0.2004 Moderately Informative Inherited
Biological Process (BP) reproduction 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.9815 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) tRNA metabolic process 0 Informative Direct
Biological Process (BP) water-soluble vitamin biosynthetic process 0.00000003575 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 0.0000000000001202 Informative Direct
Biological Process (BP) monocarboxylic acid biosynthetic process 0.0004399 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.000000000125 Informative Direct
Biological Process (BP) glycerolipid metabolic process 0.0000005566 Informative Direct
Biological Process (BP) phospholipid metabolic process 0.00000008018 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 1 Informative Inherited
Biological Process (BP) central nervous system development 0.8654 Informative Inherited
Biological Process (BP) animal organ morphogenesis 1 Informative Inherited
Biological Process (BP) post-embryonic development 0.05697 Informative Inherited
Biological Process (BP) single organism reproductive process 1 Informative Inherited
Biological Process (BP) reproductive system development 0.01794 Informative Inherited
Biological Process (BP) amine metabolic process 0.5313 Informative Inherited
Biological Process (BP) alcohol metabolic process 1 Informative Inherited
Biological Process (BP) pyridine-containing compound metabolic process 0.01591 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.03465 Informative Inherited
Biological Process (BP) purine-containing compound biosynthetic process 0.5894 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.2429 Informative Inherited
Biological Process (BP) embryo development 1 Informative Inherited
Biological Process (BP) oxidoreduction coenzyme metabolic process 1 Informative Inherited
Biological Process (BP) ribose phosphate biosynthetic process 0.008441 Informative Inherited
Biological Process (BP) liposaccharide metabolic process 0.0967 Informative Inherited
Biological Process (BP) polysaccharide metabolic process 0.9501 Informative Inherited
Biological Process (BP) cellular carbohydrate metabolic process 1 Informative Inherited
Biological Process (BP) ammonium ion metabolic process 0.00154 Informative Inherited
Biological Process (BP) NAD metabolic process 0.000000000000505 Highly Informative Direct
Biological Process (BP) ribonucleoside bisphosphate biosynthetic process 0 Highly Informative Direct
Biological Process (BP) purine nucleoside bisphosphate biosynthetic process 0 Highly Informative Direct
Biological Process (BP) pyridine-containing compound biosynthetic process 0.000498 Highly Informative Direct
Biological Process (BP) glycerophospholipid biosynthetic process 0.0000000166 Highly Informative Direct
Biological Process (BP) phosphatidylcholine metabolic process 0.00000009783 Highly Informative Direct
Biological Process (BP) coenzyme A metabolic process 0.0000007781 Highly Informative Direct
Biological Process (BP) lipopolysaccharide metabolic process 0.0002654 Highly Informative Direct
Biological Process (BP) cellular modified amino acid biosynthetic process 0.2529 Highly Informative Inherited
Biological Process (BP) seed development 0.00333 Highly Informative Inherited
Biological Process (BP) anatomical structure homeostasis 0.01473 Highly Informative Inherited
Biological Process (BP) multicellular organismal homeostasis 0.003681 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.07415 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.1525 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.006445 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 1 Moderately Informative Inherited
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.00002475 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.00014 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.0001858 Informative Direct
Molecular Function (MF) kinase activity 1 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 1 Informative Inherited
Molecular Function (MF) RNA binding 0.013 Informative Inherited
Molecular Function (MF) acid-amino acid ligase activity 0.0004851 Highly Informative Direct
Molecular Function (MF) ATP binding 0.0000002194 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.0000002208 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.03785 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.02184 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) plastid 0.000001714 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compoun0Moderately InformativeDirect
Enzyme Commission (EC)Forming carbon-nitrogen bonds1Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep1Moderately InformativeInherited
Enzyme Commission (EC)Acid--D-amino-acid ligases (peptide synthases)0InformativeDirect
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acce1InformativeInherited
Enzyme Commission (EC)Tryptophan--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Isoleucine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Methionine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Leucine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Valine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Sulfate adenylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)FAD synthetase0Highly InformativeDirect
Enzyme Commission (EC)Arginine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Glutamate--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Acid--ammonia (or amide) ligases (amide synthases)0.00000001827Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis1Moderately InformativeInherited
Biological processProtein biosynthesis0InformativeDirect
Biological processPyridine nucleotide biosynthesis0Highly InformativeDirect
Biological processCysteine biosynthesis0.0000000006658Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DomainCoiled coil0.000000002064Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationRNA-binding1Moderately InformativeInherited
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect
Post-translational modificationtRNA-binding0Highly InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · 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 43 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 Nucleotidylyl transferase 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 43 hidden Markov models representing the Nucleotidylyl transferase 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) · UniProtKB KeyWords (KW) · Internal database links ]