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)

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Superfamily statistics

	Genomes (1,791)	Uniprot 2018_03 genome	PDB chains (SCOP 1.75)
Domains	3,982	27,221	6
Proteins	3,939	27,163	6

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Functional annotation

• General category: General
• Detailed category: General

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Enzyme Commission (EC)

Highlighted in gray are those with FDR_all>0.001

	EC term	FDR (all)	IC level	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Carbon-carbon lyases	0	0.8275	--	DIRECT
Enzyme Commission (EC)	Deoxyribodipyrimidine photo-lyase	0	2.259	--	DIRECT
Enzyme Commission (EC)	Lyases	0	0.4169	Least Informative	DIRECT
Enzyme Commission (EC)	Other carbon-carbon lyases	0	1.861	Highly Informative	DIRECT

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Xenopus Anatomy (XA)

Highlighted in gray are those with FDR_all>0.001

	XA term	FDR (all)	IC level	SDXA level	Annotation (direct or inherited)
Xenopus ANatomical entity (XAN)	trunk region	0	0.4287	--	DIRECT
Xenopus ANatomical entity (XAN)	genital system	0	0.5909	--	DIRECT
Xenopus ANatomical entity (XAN)	male genitalia	0	0.8318	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical structure	0	0	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical group	0	0.1442	--	DIRECT
Xenopus ANatomical entity (XAN)	male organism	0	0.8318	--	DIRECT
Xenopus ANatomical entity (XAN)	primary germ layer	0	0.7237	--	DIRECT
Xenopus ANatomical entity (XAN)	cell	0	0.7974	--	DIRECT
Xenopus ANatomical entity (XAN)	organism subdivision	0	0.1871	--	DIRECT
Xenopus ANatomical entity (XAN)	compound organ	0	0.24	--	DIRECT
Xenopus ANatomical entity (XAN)	gonad	0	0.8318	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical region	0	0.193	--	DIRECT
Xenopus ANatomical entity (XAN)	multicellular anatomical structure	0	0.1217	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical system	1	0.3094	--	INHERITED FROM: testis || urogenital system || genital system || male genitalia
Xenopus ANatomical entity (XAN)	whole organism	1	0.09747	--	INHERITED FROM: urogenital system || genital system || anatomical group || testis || cavitated compound organ || multicellular anatomical structure || gonad || compound organ || trunk || tissue || anatomical region || male genitalia || trunk region || male organism || organism subdivision || cell || primary germ layer
Xenopus ANatomical entity (XAN)	embryo	0	0.6341	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	urogenital system	0	0.5011	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	trunk	0	0.4308	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	tissue	0	0.5011	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	cavitated compound organ	0	0.3033	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	testis	0	0.8318	Moderately Informative	DIRECT
Xenopus DEvelopment stage (XDE)	NF stage	0	0.02327	--	DIRECT

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Arabidopsis Plant Ontology (AP)

Highlighted in gray are those with FDR_all>0.001

	AP term	FDR (all)	IC level	SDAP level	Annotation (direct or inherited)
Plant ANatomical entity (PAN)	branch	0	0.6366	--	DIRECT
Plant ANatomical entity (PAN)	vascular leaf	0	0.5246	--	DIRECT
Plant ANatomical entity (PAN)	collective leaf structure	0	0.55	--	DIRECT
Plant ANatomical entity (PAN)	shoot apex	0	0.5633	--	DIRECT
Plant ANatomical entity (PAN)	stomatal complex	0	0.2774	--	DIRECT
Plant ANatomical entity (PAN)	sepal	0	0.5715	--	DIRECT
Plant ANatomical entity (PAN)	root	0	0.5579	--	DIRECT
Plant ANatomical entity (PAN)	multi-tissue plant structure	0	0.2691	--	DIRECT
Plant ANatomical entity (PAN)	plant axis	0	0.3881	--	DIRECT
Plant ANatomical entity (PAN)	leaf apex	0	0.7094	--	DIRECT
Plant ANatomical entity (PAN)	carpel	0	0.6087	--	DIRECT
Plant ANatomical entity (PAN)	plant organ	0	0.2816	--	DIRECT
Plant ANatomical entity (PAN)	calyx	0	0.5715	--	DIRECT
Plant ANatomical entity (PAN)	petal	0	0.594	--	DIRECT
Plant ANatomical entity (PAN)	leaf lamina base	0	0.7094	--	DIRECT
Plant ANatomical entity (PAN)	portion of plant tissue	0	0.1892	--	DIRECT
Plant ANatomical entity (PAN)	inflorescence axis	0	0.6366	--	DIRECT
Plant ANatomical entity (PAN)	collective plant structure	0	0.01577	--	DIRECT
Plant ANatomical entity (PAN)	pedicel	0	0.6366	--	DIRECT
Plant ANatomical entity (PAN)	epidermis	0	0.2464	--	DIRECT
Plant ANatomical entity (PAN)	plant cell	0	0.1489	--	DIRECT
Plant ANatomical entity (PAN)	reproductive shoot system	0	0.4141	--	DIRECT
Plant ANatomical entity (PAN)	androecium	0	0.594	--	DIRECT
Plant ANatomical entity (PAN)	shoot epidermal cell	0	0.276	--	DIRECT
Plant ANatomical entity (PAN)	microgametophyte	0	0.7531	--	DIRECT
Plant ANatomical entity (PAN)	shoot system	0	0.05747	--	DIRECT
Plant ANatomical entity (PAN)	microsporangium	0	0.7448	--	DIRECT
Plant ANatomical entity (PAN)	lamina	0	0.7057	--	DIRECT
Plant ANatomical entity (PAN)	cauline leaf	0	0.7019	--	DIRECT
Plant ANatomical entity (PAN)	sporophyll	0	0.4713	--	DIRECT
Plant ANatomical entity (PAN)	corolla	0	0.594	--	DIRECT
Plant ANatomical entity (PAN)	phyllome	0	0.3809	--	DIRECT
Plant ANatomical entity (PAN)	shoot internode	0	0.6463	--	DIRECT
Plant ANatomical entity (PAN)	perianth	0	0.5448	--	DIRECT
Plant ANatomical entity (PAN)	cardinal organ part	0	0.51	--	DIRECT
Plant ANatomical entity (PAN)	stem	0	0.577	--	DIRECT
Plant ANatomical entity (PAN)	shoot epidermis	0	0.2691	--	DIRECT
Plant ANatomical entity (PAN)	epidermal cell	0	0.2569	--	DIRECT
Plant ANatomical entity (PAN)	stamen	0	0.6028	--	DIRECT
Plant ANatomical entity (PAN)	phyllome apex	0	0.7019	--	DIRECT
Plant ANatomical entity (PAN)	stem internode	0	0.6495	--	DIRECT
Plant ANatomical entity (PAN)	inflorescence branch	0	0.6366	--	DIRECT
Plant ANatomical entity (PAN)	petiole	0	0.7287	--	DIRECT
Plant ANatomical entity (PAN)	gynoecium	0	0.6058	--	DIRECT
Plant ANatomical entity (PAN)	leaf lamina	0	0.7057	--	DIRECT
Plant ANatomical entity (PAN)	pollen sac	0	0.7531	--	DIRECT
Plant ANatomical entity (PAN)	plant embryo	0	0.5969	--	DIRECT
Plant ANatomical entity (PAN)	stalk	0	0.7019	--	DIRECT
Plant ANatomical entity (PAN)	phyllome lamina	1	0.7057	--	INHERITED FROM: leaf lamina base || leaf lamina
Plant ANatomical entity (PAN)	plant structure	1	0	--	INHERITED FROM: perianth || root || sporophyll || calyx || inflorescence axis || flower || lamina || collective plant structure || plant embryo || leaf || shoot internode || phyllome || pollen sac || cardinal organ part || multi-tissue plant structure || microsporophyll || guard cell || megasporophyll || cauline leaf || reproductive shoot system || shoot apex || leaf apex || leaf lamina base || branch || collective leaf structure || stem internode || inflorescence branch || shoot system || sporangium || portion of plant tissue || stomatal complex || plant organ || stem || whole plant || epidermis || root system || inflorescence || cardinal part of multi-tissue plant structure || petiole || stalk || gynoecium || vascular leaf || sepal || microsporangium || epidermal cell || leaf lamina || shoot epidermal cell || corolla || pollen || plant axis || collective phyllome structure || petal || plant cell || carpel || seed || shoot epidermis || phyllome apex || cotyledon || stamen || shoot axis || microgametophyte || pedicel || androecium
Plant ANatomical entity (PAN)	collective plant organ structure	1	0.04502	--	INHERITED FROM: inflorescence axis || calyx || flower || sporophyll || root system || inflorescence || root || perianth || stem || leaf || phyllome || shoot internode || sepal || vascular leaf || gynoecium || petiole || petal || reproductive shoot system || shoot apex || leaf apex || carpel || collective phyllome structure || guard cell || megasporophyll || cauline leaf || pollen || microsporophyll || pollen sac || leaf lamina || shoot epidermal cell || corolla || pedicel || androecium || stomatal complex || phyllome apex || cotyledon || stamen || stem internode || inflorescence branch || shoot axis || shoot system || leaf lamina base || collective leaf structure || branch || shoot epidermis
Plant ANatomical entity (PAN)	organ lamina	1	0.7057	--	INHERITED FROM: leaf lamina base || leaf lamina
Plant ANatomical entity (PAN)	inflorescence	0	0.5969	Least Informative	DIRECT
Plant ANatomical entity (PAN)	microsporophyll	0	0.5029	Least Informative	DIRECT
Plant ANatomical entity (PAN)	flower	0	0.4337	Least Informative	DIRECT
Plant ANatomical entity (PAN)	cardinal part of multi-tissue plant structure	0	0.5029	Least Informative	DIRECT
Plant ANatomical entity (PAN)	root system	0	0.5346	Least Informative	DIRECT
Plant ANatomical entity (PAN)	shoot axis	0	0.4735	Least Informative	DIRECT
Plant ANatomical entity (PAN)	sporangium	0	0.7407	Least Informative	DIRECT
Plant ANatomical entity (PAN)	whole plant	0	0.4218	Least Informative	DIRECT
Plant ANatomical entity (PAN)	seed	0	0.6087	Least Informative	DIRECT
Plant ANatomical entity (PAN)	guard cell	0	0.2774	Least Informative	DIRECT
Plant ANatomical entity (PAN)	collective phyllome structure	0	0.4648	Least Informative	DIRECT
Plant ANatomical entity (PAN)	megasporophyll	0	0.6087	Least Informative	DIRECT
Plant ANatomical entity (PAN)	leaf	0	0.5053	Least Informative	DIRECT
Plant ANatomical entity (PAN)	pollen	0	0.7531	Moderately Informative	DIRECT
Plant ANatomical entity (PAN)	cotyledon	0	0.7615	Moderately Informative	DIRECT
Plant structure DEvelopment stage (PDE)	reproductive shoot system development stage	0	0.05008	--	DIRECT
Plant structure DEvelopment stage (PDE)	phyllome development stage	0	0.4754	--	DIRECT
Plant structure DEvelopment stage (PDE)	collective phyllome structure development stage	0	0.0937	--	DIRECT
Plant structure DEvelopment stage (PDE)	sporophyte vegetative stage	0	0.2036	--	DIRECT
Plant structure DEvelopment stage (PDE)	flowering stage	0	0.2162	--	DIRECT
Plant structure DEvelopment stage (PDE)	corolla development stage	0	0.1981	--	DIRECT
Plant structure DEvelopment stage (PDE)	floral organ differentiation stage	0	0.0937	--	DIRECT
Plant structure DEvelopment stage (PDE)	floral organ formation stage	0	0.0937	--	DIRECT
Plant structure DEvelopment stage (PDE)	collective plant organ structure development stage	0	0.03771	--	DIRECT
Plant structure DEvelopment stage (PDE)	plant embryo stage	0	0.2833	--	DIRECT
Plant structure DEvelopment stage (PDE)	plant organ development stage	0	0.08108	--	DIRECT
Plant structure DEvelopment stage (PDE)	whole plant development stage	0	0.1968	--	DIRECT
Plant structure DEvelopment stage (PDE)	1 main shoot growth stage	0	0.3937	--	DIRECT
Plant structure DEvelopment stage (PDE)	leaf production stage	0	0.3937	--	DIRECT
Plant structure DEvelopment stage (PDE)	sporophyte development stage	1	0.2022	--	INHERITED FROM: E expanded cotyledon stage || LP.10 ten leaves visible stage || sporophyte vegetative stage || C globular stage || leaf production stage || 1 main shoot growth stage || D bilateral stage || F mature embryo stage || LP.04 four leaves visible stage || plant embryo stage || LP.02 two leaves visible stage
Plant structure DEvelopment stage (PDE)	shoot system development stage	1	0.04053	--	INHERITED FROM: phyllome development stage || reproductive shoot system development stage || floral organ formation stage || floral organ differentiation stage || flowering stage || corolla development stage || plant organ development stage || 4 leaf senescence stage
Plant structure DEvelopment stage (PDE)	leaf development stage	1	0.4754	--	INHERITED FROM: 4 leaf senescence stage
Plant structure DEvelopment stage (PDE)	flower development stage	1	0.07083	--	INHERITED FROM: corolla development stage || flowering stage || floral organ differentiation stage || floral organ formation stage
Plant structure DEvelopment stage (PDE)	life of whole plant stage	1	0.2022	--	INHERITED FROM: sporophyte vegetative stage || C globular stage || LP.10 ten leaves visible stage || E expanded cotyledon stage || F mature embryo stage || LP.04 four leaves visible stage || D bilateral stage || LP.02 two leaves visible stage || plant embryo stage || leaf production stage || 1 main shoot growth stage
Plant structure DEvelopment stage (PDE)	C globular stage	0	0.3937	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.10 ten leaves visible stage	0	0.513	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	E expanded cotyledon stage	0	0.353	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.04 four leaves visible stage	0	0.4338	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	F mature embryo stage	0	0.4088	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.02 two leaves visible stage	0	0.5603	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	D bilateral stage	0	0.3729	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	4 leaf senescence stage	0	0.478	Least Informative	DIRECT

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Enzyme Commission (EC)

Highlighted in gray are those with FDR_all>0.001

	EC term	FDR (all)	IC level	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Deoxyribodipyrimidine photo-lyase	0	2.651	--	DIRECT
Enzyme Commission (EC)	(6-4)DNA photolyase	0.00002188	2.952	--	DIRECT
Enzyme Commission (EC)	Lyases	0	0.6918	Least Informative	DIRECT
Enzyme Commission (EC)	Carbon-carbon lyases	0	1.101	Moderately Informative	DIRECT
Enzyme Commission (EC)	Other carbon-carbon lyases	0	1.998	Highly Informative	DIRECT

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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

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