SUPERFAMILY 1.75 HMM library and genome assignments server


Cryptochrome/photolyase, N-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Cryptochrome/photolyase, N-terminal domain [ 52424]
Superfamily:   Cryptochrome/photolyase, N-terminal domain [ 52425]
Families:   Cryptochrome/photolyase, N-terminal domain [ 52426] (2)


Superfamily statistics
Genomes (1,734) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 3,204 6,126 6
Proteins 3,190 6,116 6


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) response to stimulus 3.14e-07 Least Informative Direct
Biological Process (BP) regulation of cellular process 8.494e-07 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.08391 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.2747 Least Informative Inherited
Biological Process (BP) localization 0.488 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.001648 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.001522 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.0132 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.01916 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.02217 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.03204 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 7.96e-12 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 2.031e-11 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 4.725e-11 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 4.883e-11 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 3.039e-09 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 2.479e-06 Moderately Informative Direct
Biological Process (BP) cellular localization 0.07393 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.002904 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.002564 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.4243 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.001059 Moderately Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0 Informative Direct
Biological Process (BP) response to light stimulus 0 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0 Informative Direct
Biological Process (BP) negative regulation of gene expression 0 Informative Direct
Biological Process (BP) protein localization to organelle 6.185e-06 Informative Direct
Biological Process (BP) DNA metabolic process 7.586e-06 Informative Direct
Biological Process (BP) cytoplasmic transport 2.823e-05 Informative Direct
Biological Process (BP) protein transport 7.106e-05 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0.005449 Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-dependent 0 Highly Informative Direct
Biological Process (BP) protein targeting to nucleus 6.579e-09 Highly Informative Direct
Biological Process (BP) nuclear import 7.634e-09 Highly Informative Direct
Biological Process (BP) protein localization to nucleus 2.419e-08 Highly Informative Direct
Biological Process (BP) protein import 4.029e-08 Highly Informative Direct
Biological Process (BP) cellular response to radiation 0.0001009 Highly Informative Direct
Molecular Function (MF) binding 0.003022 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 2.385e-09 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 1 Moderately Informative Inherited
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) cofactor binding 1.491e-12 Informative Direct
Molecular Function (MF) nucleotide binding 1.615e-11 Informative Direct
Molecular Function (MF) receptor activity 1.134e-07 Informative Direct
Molecular Function (MF) molecular transducer activity 1.792e-07 Informative Direct
Molecular Function (MF) DNA binding 0.06495 Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 2.82e-06 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.02113 Least Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Other carbon-carbon lyases0Highly 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)guard cell0Least InformativeDirect
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.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible 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)Lyases0Least InformativeDirect
Enzyme Commission (EC)Carbon-carbon lyases0Moderately InformativeDirect
Enzyme Commission (EC)Other carbon-carbon lyases0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processTranscription regulation0Moderately InformativeDirect
Biological processSensory transduction0InformativeDirect
Biological processBiological rhythms0Highly InformativeDirect
Cellular componentNucleus1.264e-10Least InformativeDirect
DomainTransit peptide0.0001896Moderately InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionNucleotide-binding2.395e-05Least InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionChromophore0InformativeDirect
Molecular functionFAD0InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationLyase3.158e-14Moderately InformativeDirect
Post-translational modificationPhotoreceptor protein0Highly InformativeDirect
Post-translational modificationIsopeptide bond2.125e-10Moderately InformativeDirect
Post-translational modificationUbl conjugation5.857e-09Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR006050 SSF52425 Protein matches
Abstract

DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation [PubMed6325459]. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light [PubMed3000886]. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain [PubMed6325459]. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [PubMed3000886, PubMed2110564]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm [PubMed2110564].

This domain binds a light harvesting cofactor.


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) · 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 5 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 Cryptochrome/photolyase, N-terminal 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 5 hidden Markov models representing the Cryptochrome/photolyase, N-terminal 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]