SUPERFAMILY 1.75 HMM library and genome assignments server


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 (3,209) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8,029 0 14
Proteins 7,983 0 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 0.0001335 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.9707 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 0.6441 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.07376 Least Informative Inherited
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.1024 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.01925 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.1825 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.7419 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.001898 Moderately Informative Inherited
Biological Process (BP) gene expression 0.9743 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.6087 Moderately Informative Inherited
Biological Process (BP) immune system process 0.3161 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.6445 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) RNA processing 0.0002169 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) mitochondrion organization 0.0009407 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.01313 Informative Inherited
Biological Process (BP) chromosome organization 0.01345 Informative Inherited
Biological Process (BP) double-strand break repair 0.0005121 Highly Informative Direct
Biological Process (BP) mRNA processing 0.0006758 Highly Informative Direct
Biological Process (BP) response to ionizing radiation 9.973e-08 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 1.357e-06 Highly Informative Direct
Biological Process (BP) DNA recombination 0.3346 Highly Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.04157 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 5.517e-09 Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 2.859e-08 Least Informative Direct
Cellular Component (CC) intracellular organelle part 6.865e-05 Least Informative Direct
Cellular Component (CC) protein complex 0.1268 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.2363 Least Informative Inherited
Cellular Component (CC) nuclear part 8.873e-06 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.006713 Moderately Informative Inherited
Cellular Component (CC) chromosome 1.769e-05 Informative Direct
Cellular Component (CC) condensed chromosome 0.0001516 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.001953 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(+))1.541e-11Highly InformativeDirect
Enzyme Commission (EC)Polynucleotide 5'-phosphatase1.154e-06Highly 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 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 lethal7.753e-05Moderately InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.0001091Moderately InformativeDirect
Worm Phenotype (WP)receptor mediated endocytosis defective1.892e-05InformativeDirect

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'-phosphatase9.707e-14Highly InformativeDirect
Enzyme Commission (EC)mRNA (guanine-N(7)-)-methyltransferase2.247e-06Highly 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 ]