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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 (1,783) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,912 15,483 6
Proteins 3,874 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 0.000000000001332 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.00003295 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.00005954 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.0009701 Least Informative Direct
Biological Process (BP) biosynthetic process 0.6441 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.1053 Least Informative Inherited
Biological Process (BP) localization 0.2205 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.6724 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.001783 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.1613 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.1674 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.1799 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.2388 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.000000000000003755 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.00000000000004773 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.0000000001083 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.0000000002798 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0000000007207 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0000000008343 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.000001395 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.000004065 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.00001152 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.00005897 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.0002883 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.0006812 Moderately Informative Direct
Biological Process (BP) cellular localization 0.04872 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.3633 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.03081 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.3515 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.6225 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.3339 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.00703 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.01211 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.006276 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 0.0000000817 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.000000251 Informative Direct
Biological Process (BP) cytoplasmic transport 0.0000006681 Informative Direct
Biological Process (BP) protein transport 0.000002293 Informative Direct
Biological Process (BP) hexose metabolic process 0.000004789 Informative Direct
Biological Process (BP) response to organonitrogen compound 0.00001593 Informative Direct
Biological Process (BP) response to hormone stimulus 0.00006909 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0.00007981 Informative Direct
Biological Process (BP) DNA metabolic process 0.0001842 Informative Direct
Biological Process (BP) negative regulation of signaling 0.002839 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.005297 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.007783 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.1807 Informative Inherited
Biological Process (BP) phosphorylation 0.004627 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 0.00000000000707 Highly Informative Direct
Biological Process (BP) nuclear import 0.000000000008623 Highly Informative Direct
Biological Process (BP) protein localization to nucleus 0.00000000004295 Highly Informative Direct
Biological Process (BP) protein import 0.00000000008742 Highly Informative Direct
Biological Process (BP) regulation of protein ubiquitination 0.00000001224 Highly Informative Direct
Biological Process (BP) response to peptide hormone stimulus 0.0000000384 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.0000007556 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.000001806 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.00001263 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 0.0001245 Highly Informative Direct
Biological Process (BP) protein phosphorylation 0.0009798 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0009924 Highly Informative Direct
Biological Process (BP) cellular response to radiation 0.001477 Highly Informative Inherited
Molecular Function (MF) binding 0.02162 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.00000000312 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 0.0000000000001848 Informative Direct
Molecular Function (MF) nucleotide binding 0.00000000001436 Informative Direct
Molecular Function (MF) receptor activity 0.0000001228 Informative Direct
Molecular Function (MF) molecular transducer activity 0.000000194 Informative Direct
Molecular Function (MF) DNA binding 0.03423 Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 0.000000007517 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0007367 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.243 Least Informative Inherited
Cellular Component (CC) endomembrane system 0.0006197 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.005041 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.06648 Moderately Informative Inherited
Cellular Component (CC) nuclear envelope 0.0000665 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 ]