SUPERFAMILY 1.75 HMM library and genome assignments server


GIY-YIG endonuclease superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   GIY-YIG endonuclease [ 82770]
Superfamily:   GIY-YIG endonuclease [ 82771]
Families:   GIY-YIG endonuclease [ 82772]


Superfamily statistics
Genomes (2,849) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 5,829 16,288 2
Proteins 5,829 16,287 2


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) single-organism cellular process 0.5349 Least Informative Inherited
Biological Process (BP) response to stimulus 0.2477 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.02507 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.05393 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.1045 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.02308 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.03501 Least Informative Inherited
Biological Process (BP) cellular response to stress 4.996e-05 Moderately Informative Direct
Biological Process (BP) DNA metabolic process 3.632e-05 Informative Direct
Biological Process (BP) response to DNA damage stimulus 3.553e-07 Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processDNA recombination2.708e-12InformativeDirect
Biological processSOS response0Highly InformativeDirect
Biological processDNA excision0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DomainZinc-finger6.459e-07Moderately InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000305 SSF82771 Protein matches
Abstract

It is found in the amino terminal region of excinuclease abc subunit c (uvrC), Bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage.


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-coverage) · 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 GIY-YIG endonuclease 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 GIY-YIG endonuclease 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-coverage) · UniProtKB KeyWords (KW) · Internal database links ]