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 (1,782) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,908 15,483 6
Proteins 3,870 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 1.244e-12 Least Informative Direct
Biological Process (BP) regulation of cellular process 3.049e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 5.955e-05 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.000931 Least Informative Direct
Biological Process (BP) biosynthetic process 0.6429 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.1048 Least Informative Inherited
Biological Process (BP) localization 0.2161 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.6695 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.001746 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.1612 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.1671 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.1796 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.2385 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 3.741e-15 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 4.763e-14 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 1.006e-10 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 2.609e-10 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 6.622e-10 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 7.21e-10 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 1.215e-06 Moderately Informative Direct
Biological Process (BP) cellular response to stress 3.754e-06 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 1.065e-05 Moderately Informative Direct
Biological Process (BP) macromolecule localization 5.866e-05 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.0002874 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.0006564 Moderately Informative Direct
Biological Process (BP) cellular localization 0.04825 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.3595 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.02994 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.3496 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.6215 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.3413 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.006958 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.01219 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.006255 Moderately Informative Inherited
Biological Process (BP) negative regulation of gene expression 0 Informative Direct
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) protein localization to organelle 7.909e-08 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 2.512e-07 Informative Direct
Biological Process (BP) cytoplasmic transport 6.54e-07 Informative Direct
Biological Process (BP) protein transport 2.298e-06 Informative Direct
Biological Process (BP) hexose metabolic process 4.787e-06 Informative Direct
Biological Process (BP) response to organonitrogen compound 1.559e-05 Informative Direct
Biological Process (BP) response to hormone stimulus 6.68e-05 Informative Direct
Biological Process (BP) response to DNA damage stimulus 8.577e-05 Informative Direct
Biological Process (BP) DNA metabolic process 0.0001871 Informative Direct
Biological Process (BP) negative regulation of signaling 0.002659 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.005008 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.007497 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.1878 Informative Inherited
Biological Process (BP) phosphorylation 0.004601 Informative Inherited
Biological Process (BP) circadian rhythm 0 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 0 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0 Highly Informative Direct
Biological Process (BP) protein targeting to nucleus 6.902e-12 Highly Informative Direct
Biological Process (BP) nuclear import 8.431e-12 Highly Informative Direct
Biological Process (BP) protein localization to nucleus 4.059e-11 Highly Informative Direct
Biological Process (BP) protein import 8.62e-11 Highly Informative Direct
Biological Process (BP) regulation of protein ubiquitination 1.152e-08 Highly Informative Direct
Biological Process (BP) response to peptide hormone stimulus 3.56e-08 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 6.945e-07 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 1.651e-06 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 1.477e-05 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 0.0001242 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0009581 Highly Informative Direct
Biological Process (BP) protein phosphorylation 0.0009895 Highly Informative Direct
Biological Process (BP) cellular response to radiation 0.001369 Highly Informative Inherited
Molecular Function (MF) binding 0.0208 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 2.934e-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 1.795e-13 Informative Direct
Molecular Function (MF) nucleotide binding 1.376e-11 Informative Direct
Molecular Function (MF) receptor activity 1.237e-07 Informative Direct
Molecular Function (MF) molecular transducer activity 1.93e-07 Informative Direct
Molecular Function (MF) DNA binding 0.03321 Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 6.294e-09 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0007142 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.2432 Least Informative Inherited
Cellular Component (CC) endomembrane system 0.0004492 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.005058 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.06733 Moderately Informative Inherited
Cellular Component (CC) nuclear envelope 7.017e-05 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 componentNucleus4.156e-11Least InformativeDirect
DomainTransit peptide0.0002443Moderately InformativeDirect
Molecular functionNucleotide-binding9.503e-06Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionChromophore0InformativeDirect
Molecular functionFAD0InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationLyase6.008e-14Moderately InformativeDirect
Post-translational modificationPhotoreceptor protein0Highly InformativeDirect
Post-translational modificationIsopeptide bond3.499e-10Moderately InformativeDirect
Post-translational modificationUbl conjugation9.539e-09Moderately 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 ]