SUPERFAMILY 1.75 HMM library and genome assignments server

Please note: Superfamily is currently under maintenance and some functionality may be limited. Please bear with us as we fix these problems.


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 (3,214) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8,059 31,391 14
Proteins 8,012 31,306 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 aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0.00001757 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.9643 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.7396 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.07097 Least Informative Inherited
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.8688 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.02023 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.1851 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.8178 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.002744 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.5927 Moderately Informative Inherited
Biological Process (BP) immune system process 0.304 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.6307 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) RNA processing 0.0007567 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) mitochondrion organization 0.0009203 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.01348 Informative Inherited
Biological Process (BP) chromosome organization 0.01317 Informative Inherited
Biological Process (BP) double-strand break repair 0.0003478 Highly Informative Direct
Biological Process (BP) mRNA processing 0.0006469 Highly Informative Direct
Biological Process (BP) response to ionizing radiation 0.00000009815 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.000001229 Highly Informative Direct
Biological Process (BP) DNA recombination 0.4575 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.9829 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.02405 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0.0000000002468 Informative Direct
Molecular Function (MF) ligase activity 0 Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0000002682 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00005489 Least Informative Direct
Cellular Component (CC) protein complex 0.1313 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.2376 Least Informative Inherited
Cellular Component (CC) nuclear part 0.000003875 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.009012 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.000007512 Informative Direct
Cellular Component (CC) nuclear chromosome part 0.001676 Highly Informative Inherited

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

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)growth/size/body phenotype0Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal metabolism0Moderately InformativeDirect
Mammalian Phenotype (MP)preweaning lethality0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal cell proliferation0InformativeDirect
Mammalian Phenotype (MP)abnormal prenatal growth/weight/body size0InformativeDirect
Mammalian Phenotype (MP)lethality during fetal growth through weaning0InformativeDirect
Mammalian Phenotype (MP)postnatal growth retardation0Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0Least InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.00007753Moderately InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.0001091Moderately InformativeDirect
Worm Phenotype (WP)receptor mediated endocytosis defective0.00001892InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases1Moderately InformativeInherited
Enzyme Commission (EC)mRNA guanylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Polynucleotide 5'-phosphatase0.00000000000009463Highly InformativeDirect
Enzyme Commission (EC)mRNA (guanine-N(7)-)-methyltransferase0.000002214Highly InformativeDirect
Enzyme Commission (EC)Ligases that form phosphoric-ester bonds1Highly InformativeInherited

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 replication0InformativeDirect
Biological processmRNA capping0Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)mRNA processing0Highly InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]