SUPERFAMILY 1.75 HMM library and genome assignments server


ATP-dependent DNA ligase DNA-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   ATP-dependent DNA ligase DNA-binding domain [ 117017]
Superfamily:   ATP-dependent DNA ligase DNA-binding domain [ 117018]
Families:   ATP-dependent DNA ligase DNA-binding domain [ 117019]


Superfamily statistics
Genomes (877) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,671 2,476 1
Proteins 1,666 2,474 1


Functional annotation
General category Regulation
Detailed category DNA-binding

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 macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound 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) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) response to stimulus 9.956e-10 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0001531 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.8058 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.2713 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.001261 Least Informative Inherited
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0.000117 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.0005003 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.2808 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.01123 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.6821 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.08511 Moderately Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0 Informative Direct
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0001483 Informative Direct
Biological Process (BP) response to inorganic substance 0.0003801 Informative Direct
Biological Process (BP) mitochondrion organization 0.0005658 Informative Direct
Biological Process (BP) chromosome organization 0.0255 Informative Inherited
Biological Process (BP) regulation of DNA metabolic process 5.704e-09 Highly Informative Direct
Biological Process (BP) response to ionizing radiation 3.606e-08 Highly Informative Direct
Biological Process (BP) double-strand break repair 0.0001374 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 2.175e-11 Least Informative Direct
Cellular Component (CC) protein complex 0.2177 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.003032 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.02092 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.0001459 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.0001895 Moderately Informative Direct
Cellular Component (CC) chromosome 2.473e-05 Informative Direct
Cellular Component (CC) nuclear chromosome part 0.0002919 Highly 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)Ligases that form phosphoric-ester bonds1InformativeInherited

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

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
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)gamete0InformativeDirect
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)Ligases0Moderately 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
Cellular componentNucleus2.885e-07Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionMagnesium0.0006866Moderately InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 1 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 ATP-dependent DNA ligase DNA-binding 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 1 hidden Markov models representing the ATP-dependent DNA ligase DNA-binding 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) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]