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Nucleotidyltransferase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Nucleotidyltransferase [ 81302]
Superfamily:   Nucleotidyltransferase [ 81301] (14)
Families:   Catalytic subunit of bi-partite nucleotidyltransferase [ 102932] (3)
  Kanamycin nucleotidyltransferase (KNTase), N-terminal domain [ 56708]
  Poly(A) polymerase, PAP, N-terminal domain [ 81589]
  2'-5'-oligoadenylate synthetase 1, OAS1, N-terminal domain [ 102937]
  Archaeal tRNA CCA-adding enzyme catalytic domain [ 102940]
  DNA polymerase beta-like [ 81300] (4)
  Poly A polymerase head domain-like [ 82661] (2)
  RelA/SpoT domain [ 102945] (2)
  GlnE-like domain [ 110933]
  RNA editing terminal uridyl transferase 2, RET2, catalytic domain [ 143236]
  TM1012-like [ 143239]
  Iojap/YbeB-like [ 160252] (2)
  AadK N-terminal domain-like [ 160257]
  GrpB-like [ 160260]


Superfamily statistics
Genomes (3,207) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 29,224 158,493 42
Proteins 27,711 149,964 42


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)
Molecular Function (MF)binding10.9273Least InformativeInherited
Molecular Function (MF)nucleic acid binding0.032470.0001177Moderately InformativeInherited
Molecular Function (MF)RNA binding0.0051830InformativeInherited

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) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.000000000001244 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0001208 Least Informative Direct
Biological Process (BP) biosynthetic process 0.5761 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.9168 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.7021 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0.0000000007122 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.000000001345 Moderately Informative Direct
Biological Process (BP) response to biotic stimulus 0.000000006573 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0.00000007874 Moderately Informative Direct
Biological Process (BP) response to external stimulus 0.000009803 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.00002625 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.4715 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.3055 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.7682 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.5552 Moderately Informative Inherited
Biological Process (BP) immune system process 0.02513 Moderately Informative Inherited
Biological Process (BP) defense response 0.005711 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.6266 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.9557 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.8746 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.4213 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.05105 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.00884 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.2835 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.6787 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.5834 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.7758 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.01228 Moderately Informative Inherited
Biological Process (BP) purine-containing compound biosynthetic process 0.00000000000004251 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.000000003708 Informative Direct
Biological Process (BP) glutamine family amino acid metabolic process 0.0000000922 Informative Direct
Biological Process (BP) immune effector process 0.0000001591 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0000121 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.00007103 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0001882 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.0003804 Informative Direct
Biological Process (BP) regulation of hydrolase activity 0.003456 Informative Inherited
Biological Process (BP) defense response to other organism 0.03919 Informative Inherited
Biological Process (BP) tRNA metabolic process 0.7566 Informative Inherited
Biological Process (BP) ncRNA processing 0.5622 Informative Inherited
Biological Process (BP) DNA metabolic process 0.01133 Informative Inherited
Biological Process (BP) cellular response to DNA damage stimulus 0.001832 Informative Inherited
Biological Process (BP) response to virus 0 Highly Informative Direct
Biological Process (BP) regulation of viral process 0 Highly Informative Direct
Biological Process (BP) negative regulation of multi-organism process 0 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0.00000001588 Highly Informative Direct
Biological Process (BP) mRNA processing 0.09626 Highly Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.04647 Highly Informative Inherited
Biological Process (BP) modification-dependent macromolecule catabolic process 1 Highly Informative Inherited
Biological Process (BP) gene silencing 0.001061 Highly Informative Inherited
Biological Process (BP) double-strand break repair 0.1108 Highly Informative Inherited
Molecular Function (MF) transferase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.9273 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0001177 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.0002264 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0.0002923 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.1915 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.3635 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.00679 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.0000009628 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.00000172 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.002654 Informative Inherited
Molecular Function (MF) DNA-directed DNA polymerase activity 0 Highly Informative Direct
Molecular Function (MF) ATP binding 0.00000001167 Highly Informative Direct
Molecular Function (MF) manganese ion binding 0.0002146 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00009073 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.947 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.4911 Least Informative Inherited
Cellular Component (CC) nuclear part 0.000002852 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00007799 Moderately Informative Direct
Cellular Component (CC) nucleoplasm part 0.7224 Informative Inherited

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)Acting on ester bonds1Least InformativeInherited
Enzyme Commission (EC)Diphosphotransferases0.0000002083InformativeDirect
Enzyme Commission (EC)Polynucleotide adenylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)[Protein-PII] uridylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)GTP diphosphokinase0Highly InformativeDirect
Enzyme Commission (EC)Guanosine-3',5'-bis(diphosphate) 3'-diphosphatase0Highly InformativeDirect
Enzyme Commission (EC)CCA tRNA nucleotidyltransferase0Highly InformativeDirect
Enzyme Commission (EC)RNA uridylyltransferase0.00000000005709Highly InformativeDirect
Enzyme Commission (EC)DNA nucleotidylexotransferase0.000000002012Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processImmunity0.0000003026Moderately InformativeDirect
Biological processmRNA processing0InformativeDirect
Biological processNitrogen fixation0InformativeDirect
Biological processtRNA processing0InformativeDirect
Biological processInnate immunity0.00000000001942InformativeDirect
Biological processAntibiotic resistance0.00007585InformativeDirect
Biological processAntiviral defense0Highly InformativeDirect
Biological processDNA synthesis4.848e-16Highly InformativeDirect
Cellular componentNucleus0.0002484Least InformativeDirect
Cellular componentMitochondrion0.00003825Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.7636Moderately InformativeInherited
Cellular componentMicrosome0.000151Highly InformativeDirect
DomainRepeat0Least InformativeDirect
DomainTransit peptide0.000000000001031Moderately InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMetal-binding0.00006485Least InformativeDirect
Molecular functionManganese0.000000001084Moderately InformativeDirect
Molecular functionNickel0InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately 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 25 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 Nucleotidyltransferase 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 25 hidden Markov models representing the Nucleotidyltransferase 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 ]