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DNA ligase/mRNA capping enzyme, catalytic domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   ATP-grasp [ 56058] (2)
Superfamily:   DNA ligase/mRNA capping enzyme, catalytic domain [ 56091] (4)
Families:   ATP-dependent DNA ligase catalytic domain [ 56092] (2)
  Adenylation domain of NAD+-dependent DNA ligase [ 56096]
  mRNA capping enzyme [ 56100] (2)
  RNA ligase [ 103286] (2)


Superfamily statistics
Genomes (3,223) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 8,156 46,589 14
Proteins 8,105 46,347 14


Functional annotation
General category Information
Detailed category DNA replication/repair

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) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic 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) primary metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0.000007459 Least Informative Direct
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.0353 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.8775 Moderately Informative Inherited
Biological Process (BP) gene expression 0.8736 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) RNA modification 0.0006061 Informative Direct
Biological Process (BP) response to radiation 0.000953 Informative Direct
Biological Process (BP) mRNA processing 0.0004838 Highly Informative Direct
Biological Process (BP) double-strand break repair 0.0312 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.9624 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.0009493 Moderately Informative Direct
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.0000000000000366 Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000007289 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0003308 Least Informative Direct
Cellular Component (CC) protein complex 0.02091 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.9761 Least Informative Inherited
Cellular Component (CC) chromosome 0.0007268 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds1Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases1Least InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases1Moderately InformativeInherited
Enzyme Commission (EC)Ligases that form phosphoric-ester bonds1InformativeInherited
Enzyme Commission (EC)mRNA guanylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)DNA ligase (NAD(+))0.00000000001541Highly InformativeDirect
Enzyme Commission (EC)Polynucleotide 5'-phosphatase0.000001154Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0Moderately InformativeDirect
Biological processDNA damage0Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processDNA repair0InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processmRNA processing0.002173InformativeInherited
Biological processmRNA capping0Highly InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect

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 11 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 DNA ligase/mRNA capping enzyme, catalytic 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 11 hidden Markov models representing the DNA ligase/mRNA capping enzyme, catalytic 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 ]