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Cryptochrome/photolyase FAD-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Cryptochrome/photolyase FAD-binding domain [ 48172]
Superfamily:   Cryptochrome/photolyase FAD-binding domain [ 48173]
Families:   Cryptochrome/photolyase FAD-binding domain [ 48174] (2)


Superfamily statistics
Genomes (1,791) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 3,982 18,907 6
Proteins 3,939 18,859 6


Functional annotation
General category General
Detailed category General

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) cellular aromatic compound metabolic process 0.000176 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0007557 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0006121 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0001498 Least Informative Direct
Biological Process (BP) response to stimulus 0.000000003665 Least Informative Direct
Biological Process (BP) biological regulation 0.0000007964 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0004853 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0446 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.9176 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.9148 Least Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.000000000000003734 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0000008747 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.00001615 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.00000003372 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.00002112 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.9866 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.08263 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.07117 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.01233 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.8895 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.6694 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.5453 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.01062 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.0341 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.02903 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.08677 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.9046 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.09092 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.01435 Moderately Informative Inherited
Biological Process (BP) monosaccharide metabolic process 0.0000152 Informative Direct
Biological Process (BP) DNA metabolic process 0.00000002244 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.0000001349 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) negative regulation of gene expression 0 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.00003554 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0 Informative Direct
Biological Process (BP) protein localization to organelle 0.0000599 Informative Direct
Biological Process (BP) single-organism cellular localization 0.0004268 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0.6656 Informative Inherited
Biological Process (BP) regulation of cell cycle 0.3631 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 1 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.01701 Informative Inherited
Biological Process (BP) intracellular transport 0.009815 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.4054 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.01965 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.516 Informative Inherited
Biological Process (BP) protein transport 0.001057 Informative Inherited
Biological Process (BP) phosphorylation 0.003611 Informative Inherited
Biological Process (BP) response to oxidative stress 0.102 Informative Inherited
Biological Process (BP) glucose metabolic process 0.0000003431 Highly Informative Direct
Biological Process (BP) circadian rhythm 0.000000000000001925 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.0000009964 Highly Informative Direct
Biological Process (BP) photoperiodism 0.0002006 Highly Informative Direct
Biological Process (BP) protein import 0.0000001316 Highly Informative Direct
Biological Process (BP) hexose biosynthetic process 0.00000001072 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.000018 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.00001289 Highly Informative Direct
Biological Process (BP) protein localization to nucleus 0.00000008817 Highly Informative Direct
Biological Process (BP) response to hydrogen peroxide 0.0001498 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0 Highly Informative Direct
Biological Process (BP) response to peptide hormone 0.00001921 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0 Highly Informative Direct
Biological Process (BP) single-organism nuclear import 0.00000002225 Highly Informative Direct
Biological Process (BP) regulation of protein modification by small protein conjugation or removal 0.00002044 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.03531 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.03333 Highly Informative Inherited
Molecular Function (MF) binding 0.3996 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.000000001805 Moderately Informative Direct
Molecular Function (MF) anion binding 0.00000002081 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 1 Moderately Informative Inherited
Molecular Function (MF) signal transducer activity 0.000000002337 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) coenzyme binding 0 Informative Direct
Molecular Function (MF) molecular transducer activity 0.000000001048 Informative Direct
Molecular Function (MF) DNA binding 0.01899 Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 0.00003694 Highly Informative Direct
Cellular Component (CC) membrane 0.79 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.1721 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cell projection 0.0003215 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0.0000001975 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.4603 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.4085 Moderately Informative Inherited
Cellular Component (CC) endomembrane system 0.9627 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.3945 Moderately Informative Inherited
Cellular Component (CC) nuclear envelope 0.00005679 Informative Direct
Cellular Component (CC) cilium 0.000000001079 Informative Direct
Cellular Component (CC) neuron projection 0.00000008869 Informative Direct
Cellular Component (CC) plasma membrane region 0.000000001873 Informative Direct
Cellular Component (CC) plasma membrane bounded cell projection part 0.00000001299 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processTranscription regulation2.442e-16Moderately InformativeDirect
Biological processBiological rhythms0InformativeDirect
Biological processDNA repair0InformativeDirect
Biological processSensory transduction0InformativeDirect
Cellular componentNucleus0.0000000002277Least InformativeDirect
DomainTransit peptide0.0002972Moderately InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionChromophore0InformativeDirect
Molecular functionFAD0InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationLyase0.000000000000003702Moderately InformativeDirect
Post-translational modificationPhotoreceptor protein0Highly InformativeDirect
Post-translational modificationIsopeptide bond0.0000005723Moderately InformativeDirect
Post-translational modificationUbl conjugation0.000001137Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR005101 SSF48173 Protein matches
Abstract

Deoxyribodipyrimidine photolyase (DNA photolyase) is a DNA repair enzyme. It binds to UV-damaged DNA containing pyrimidine dimers and, upon absorbing a near-UV photon (300 to 500 nm), breaks the cyclobutane ring joining the two pyrimidines of the dimer. DNA photolyase is an enzyme that requires two choromophore-cofactors for its activity: a reduced FADH2 and either 5,10-methenyltetrahydrofolate (5,10-MTFH) or an oxidized 8-hydroxy-5- deazaflavin (8-HDF) derivative (F420). The folate or deazaflavin chromophore appears to function as an antenna, while the FADH2 chromophore is thought to be responsible for electron transfer. On the basis of sequence similarities DNA photolyases can be grouped into two classes. The first class contains enzymes from Gram-negative and Gram-positive bacteria, the halophilic archaebacteria Halobacterium halobium, fungi and plants. Class 1 enzymes bind either 5,10-MTHF (E. coli, fungi, etc.) or 8-HDF (S.griseus, H.halobium).

Proteins containing this domain also include Arabidopsis cryptochromes 1 (CRY1) and 2 (CRY2), which are blue light photoreceptors that mediate blue light-induced gene expression.


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) · 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 FAD-binding 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 FAD-binding 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) · UniProtKB KeyWords (KW) · Internal database links ]