SUPERFAMILY 1.75 HMM library and genome assignments server


Prokaryotic type I DNA topoisomerase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   Prokaryotic type I DNA topoisomerase [ 56711]
Superfamily:   Prokaryotic type I DNA topoisomerase [ 56712]
Families:   Prokaryotic type I DNA topoisomerase [ 56713] (3)


Superfamily statistics
Genomes (3,192) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,655 35,723 8
Proteins 5,602 35,662 8


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)single-organism cellular process7.346e-060.1468Least InformativeInherited
Biological Process (BP)chromosome segregation00Highly InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle1.578e-100.0002599Least InformativeDirect
Cellular Component (CC)chromosome01.508e-13InformativeDirect

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) cellular aromatic compound metabolic process 2.009e-06 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1.465e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 9.094e-05 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 1.631e-06 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 4.716e-06 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.1468 Least Informative Inherited
Biological Process (BP) DNA metabolic process 3.161e-13 Informative Direct
Biological Process (BP) chromosome segregation 0 Highly Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.0002599 Least Informative Direct
Cellular Component (CC) chromosome 1.508e-13 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides5.958e-06Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an2.586e-13Moderately InformativeDirect
Enzyme Commission (EC)Sole sub-subclass for isomerases that do not belon1InformativeInherited
Enzyme Commission (EC)DNA topoisomerase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight 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)Hydrolases0.9296Least InformativeInherited
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides7.173e-06Moderately InformativeDirect
Enzyme Commission (EC)DNA helicase0InformativeDirect
Enzyme Commission (EC)DNA topoisomerase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
DomainRepeat4.472e-06Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Post-translational modificationHydrolase0.5565Least InformativeInherited
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationHelicase0InformativeDirect
Post-translational modificationTopoisomerase0Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000380 SSF56712 Protein matches
Abstract

This entry describes the core region of type IA topoisomerases, which are highly conserved enzymes that are structurally distinct from type IB enzymes. The structures of both topoisomerases I and III have been elucidated, and consist of four domains that together form a toroidal molecule with a central hole that is large enough to accommodate single- and double-stranded DNA [PubMed11239459]. It is believed that the domains transiently separate from one another to allow the entrance and exit of DNA strands.

More information about this protein can be found at Protein of the Month: DNA Topoisomerase.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · 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 3 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 Prokaryotic type I DNA topoisomerase 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 3 hidden Markov models representing the Prokaryotic type I DNA topoisomerase 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]