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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 (1,781) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,489 13,801 6
Proteins 3,463 13,790 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 0.00000000003345 Least Informative Direct
Biological Process (BP) biological regulation 0.0000001083 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0001253 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0003482 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0004105 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0006955 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.7217 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.001874 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.0119 Least Informative Inherited
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 0 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.000000000000003692 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.00000000000005973 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0.000006785 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.00001295 Moderately Informative Direct
Biological Process (BP) regulation of nitrogen compound metabolic process 0.00001379 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.8983 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.8127 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.005771 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.3983 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.8362 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.9403 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.06815 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.01836 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.1064 Moderately Informative Inherited
Biological Process (BP) response to stress 0.01258 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.03798 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.08371 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.05047 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.02514 Moderately Informative Inherited
Biological Process (BP) regulation of transcription, DNA-templated 0 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 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) response to radiation 0 Informative Direct
Biological Process (BP) DNA metabolic process 0.0000001434 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.0000001764 Informative Direct
Biological Process (BP) monosaccharide metabolic process 0.000006585 Informative Direct
Biological Process (BP) nucleocytoplasmic transport 0.000009516 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.00001347 Informative Direct
Biological Process (BP) protein targeting 0.00005626 Informative Direct
Biological Process (BP) protein localization to organelle 0.0002097 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.0004676 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0.5671 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.2726 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.008297 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.3285 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.3975 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.9752 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.007276 Informative Inherited
Biological Process (BP) phosphorylation 0.001597 Informative Inherited
Biological Process (BP) circadian rhythm 0 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 0.00000001231 Highly Informative Direct
Biological Process (BP) glucose metabolic process 0.0000001406 Highly Informative Direct
Biological Process (BP) protein targeting to nucleus 0.0000002924 Highly Informative Direct
Biological Process (BP) single-organism nuclear import 0.0000003171 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.0000009977 Highly Informative Direct
Biological Process (BP) protein import 0.000001394 Highly Informative Direct
Biological Process (BP) response to peptide hormone 0.000004658 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.000007071 Highly Informative Direct
Biological Process (BP) regulation of protein modification by small protein conjugation or removal 0.00002119 Highly Informative Direct
Biological Process (BP) photoperiodism 0.0002212 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0286 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.02669 Highly Informative Inherited
Molecular Function (MF) binding 0.4047 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.00000006048 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0000006582 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 1 Moderately Informative Inherited
Molecular Function (MF) protein binding 0.7487 Moderately Informative Inherited
Molecular Function (MF) coenzyme binding 0 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) molecular transducer activity 0.0000000006323 Informative Direct
Molecular Function (MF) signal transducer activity 0.00000000112 Informative Direct
Molecular Function (MF) DNA binding 0.01596 Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 0.000002355 Highly Informative Direct
Cellular Component (CC) membrane 0.7509 Least Informative Inherited
Cellular Component (CC) protein complex 0.1652 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) plasma membrane 0.5746 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 0.001195 Moderately Informative Inherited
Cellular Component (CC) cell projection 0.001408 Moderately Informative Inherited
Cellular Component (CC) cilium 0.00000002865 Informative Direct
Cellular Component (CC) plasma membrane region 0.00000003229 Informative Direct
Cellular Component (CC) cell projection part 0.000004052 Informative Direct
Cellular Component (CC) 9+2 non-motile cilium 0 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)Lyases0Least InformativeDirect
Enzyme Commission (EC)Other carbon-carbon lyases0Highly InformativeDirect

Document: EC 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)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)female genitalia0Moderately 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)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence 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)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible 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.10 ten 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 regulation4.822e-16Moderately InformativeDirect
Biological processBiological rhythms0InformativeDirect
Biological processSensory transduction0InformativeDirect
Cellular componentNucleus0.0000000004048Least InformativeDirect
DomainTransit peptide0.000272Moderately InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionNucleotide-binding0.00002829Least InformativeDirect
Molecular functionFAD0InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationLyase0.000000000000006827Moderately InformativeDirect
Post-translational modificationPhotoreceptor protein0Highly InformativeDirect
Post-translational modificationIsopeptide bond0.00000002589Moderately InformativeDirect
Post-translational modificationUbl conjugation0.000000108Moderately 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) · 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 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) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]