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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 (1,786) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 3,503 14,996 6
Proteins 3,477 14,971 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 0.0000000000895 Least Informative Direct
Biological Process (BP) biological regulation 0.0000002346 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0001553 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0002761 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0003331 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0006647 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0009246 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.01586 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.7528 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 macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.000000000000003764 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0000000000000446 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.00000003571 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000003945 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.00001696 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.00006161 Moderately Informative Direct
Biological Process (BP) regulation of signaling 0.7876 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.02465 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.006864 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.1066 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.05793 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.379 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.7484 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.8881 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.928 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.02189 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.02222 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.09908 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.08935 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.04367 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0 Informative Direct
Biological Process (BP) response to radiation 0 Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0 Informative Direct
Biological Process (BP) regulation of transcription, DNA-templated 0 Informative Direct
Biological Process (BP) negative regulation of gene expression 0 Informative Direct
Biological Process (BP) DNA metabolic process 0.0000001101 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.0000004667 Informative Direct
Biological Process (BP) monosaccharide metabolic process 0.00000757 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.00001657 Informative Direct
Biological Process (BP) protein localization to organelle 0.0002521 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.0004945 Informative Direct
Biological Process (BP) intracellular protein transport 0.0008144 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.3821 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.2915 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.007954 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.01204 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.29 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.9396 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.5618 Informative Inherited
Biological Process (BP) phosphorylation 0.001536 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 transcription, DNA-templated 0 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 0.00000001755 Highly Informative Direct
Biological Process (BP) glucose metabolic process 0.0000001784 Highly Informative Direct
Biological Process (BP) protein targeting to nucleus 0.0000002741 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.000001112 Highly Informative Direct
Biological Process (BP) protein import 0.000001365 Highly Informative Direct
Biological Process (BP) response to peptide hormone 0.000005125 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.000007661 Highly Informative Direct
Biological Process (BP) regulation of protein modification by small protein conjugation or removal 0.00002253 Highly Informative Direct
Biological Process (BP) photoperiodism 0.0002251 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.02889 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.02635 Highly Informative Inherited
Molecular Function (MF) binding 0.3776 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.00000001933 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0000001514 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) coenzyme binding 0 Informative Direct
Molecular Function (MF) molecular transducer activity 0.0000000007054 Informative Direct
Molecular Function (MF) signal transducer activity 0.000000001547 Informative Direct
Molecular Function (MF) DNA binding 0.01711 Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 0.000008356 Highly Informative Direct
Cellular Component (CC) membrane 0.7995 Least Informative Inherited
Cellular Component (CC) macromolecular complex 0.787 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) bounding membrane of organelle 0.000002529 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.593 Moderately Informative Inherited
Cellular Component (CC) cell projection 0.001469 Moderately Informative Inherited
Cellular Component (CC) cilium 0.00000004031 Informative Direct
Cellular Component (CC) plasma membrane region 0.00000004409 Informative Direct
Cellular Component (CC) plasma membrane bounded cell projection part 0.0000001992 Informative Direct
Cellular Component (CC) neuron projection 0.0000007836 Informative Direct
Cellular Component (CC) photoreceptor cell 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)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least 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)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo 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 regulation7.253e-16Moderately InformativeDirect
Biological processBiological rhythms0InformativeDirect
Biological processSensory transduction0InformativeDirect
Cellular componentNucleus0.0000000004804Least InformativeDirect
DomainTransit peptide0.000212Moderately InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionChromophore0InformativeDirect
Molecular functionFAD0InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationLyase0.00000000000001416Moderately InformativeDirect
Post-translational modificationPhotoreceptor protein0Highly InformativeDirect
Post-translational modificationIsopeptide bond0.00000002537Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0000001292Moderately 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 ]