SUPERFAMILY 1.75 HMM library and genome assignments server

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 (1,784) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,935 15,483 6
Proteins 3,897 15,466 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) response to stimulus 0.00000000000131 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.00003824 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.00004808 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0008355 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.001463 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.6254 Least Informative Inherited
Biological Process (BP) localization 0.2396 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.08018 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.05622 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.6774 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.1629 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.1697 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.1815 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.2384 Least Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.00000000000005029 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.00000000000005349 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.0000000001174 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.0000000003026 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0000000008653 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.000000002345 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.000002065 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.000004534 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.00001191 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.00005479 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.000295 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.0007165 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.7565 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.3535 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.002291 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.02831 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.3331 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.006198 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.3688 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.08972 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.007129 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.01602 Moderately Informative Inherited
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) response to light stimulus 0 Informative Direct
Biological Process (BP) DNA repair 0.0000000004771 Informative Direct
Biological Process (BP) protein localization to organelle 0.00000008856 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.0000002483 Informative Direct
Biological Process (BP) cytoplasmic transport 0.0000009598 Informative Direct
Biological Process (BP) hexose metabolic process 0.000002109 Informative Direct
Biological Process (BP) single-organism cellular localization 0.000002152 Informative Direct
Biological Process (BP) protein transport 0.000002361 Informative Direct
Biological Process (BP) response to organonitrogen compound 0.00001602 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.00002593 Informative Direct
Biological Process (BP) regulation of cell cycle process 0.00006642 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.006939 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.01068 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.2398 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.003719 Informative Inherited
Biological Process (BP) phosphorylation 0.007621 Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-templated 0 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0 Highly Informative Direct
Biological Process (BP) circadian rhythm 0 Highly Informative Direct
Biological Process (BP) protein targeting to nucleus 0.000000000007014 Highly Informative Direct
Biological Process (BP) single-organism nuclear import 0.000000000007132 Highly Informative Direct
Biological Process (BP) protein import 0.00000000008649 Highly Informative Direct
Biological Process (BP) regulation of protein ubiquitination 0.00000001422 Highly Informative Direct
Biological Process (BP) response to peptide hormone 0.00000003844 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.0000007581 Highly Informative Direct
Biological Process (BP) glucose metabolic process 0.0000007697 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.00001346 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 0.000193 Highly Informative Direct
Biological Process (BP) protein phosphorylation 0.0007086 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.001072 Highly Informative Inherited
Biological Process (BP) cellular response to radiation 0.002125 Highly Informative Inherited
Molecular Function (MF) binding 0.02306 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.000000003149 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.000000008613 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 0.0000000000001722 Informative Direct
Molecular Function (MF) nucleotide binding 0.00000000001438 Informative Direct
Molecular Function (MF) receptor activity 0.00000009352 Informative Direct
Molecular Function (MF) molecular transducer activity 0.0000001492 Informative Direct
Molecular Function (MF) DNA binding 0.0187 Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 0.000000008864 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.599 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.001408 Least Informative Inherited
Cellular Component (CC) organelle envelope 0.00409 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.1577 Moderately Informative Inherited
Cellular Component (CC) nuclear envelope 0.000002321 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

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo 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)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence 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 processBiological rhythms0InformativeDirect
Biological processSensory transduction0InformativeDirect
Cellular componentNucleus0.00000000004289Least InformativeDirect
DomainTransit peptide0.0002472Moderately InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionNucleotide-binding0.000008977Least InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionChromophore0InformativeDirect
Molecular functionFAD0InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationLyase0.000000000000065Moderately InformativeDirect
Post-translational modificationPhotoreceptor protein0Highly InformativeDirect
Post-translational modificationIsopeptide bond0.0000000003751Moderately InformativeDirect
Post-translational modificationUbl conjugation0.00000001013Moderately 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) · 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 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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]