GAF domain family

SCOP classification

• Root: SCOP hierarchy in SUPERFAMILY [ 0] (11)
• Class: Alpha and beta proteins (a+b) [ 53931] (376)
• Fold: Profilin-like [ 55769] (10)
• Superfamily: GAF domain-like [ 55781] (4)
• Family: GAF domain [ 55782] (7)

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Family statistics

	Genomes (1,630)	Uniprot 2018_03 genome	PDB chains (SCOP 1.75)
Domains	2,876	23,035	11
Proteins	2,731	22,549	10

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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)	3',5'-cyclic-GMP phosphodiesterase	0	2.44	--	DIRECT
Enzyme Commission (EC)	Hydrolases	0.00000000001185	0.01852	--	DIRECT
Enzyme Commission (EC)	Transferring phosphorous-containing groups	0.00000008381	0.2728	--	DIRECT
Enzyme Commission (EC)	Transferases	0.1508	0	--	INHERITED FROM: Transferring phosphorous-containing groups || Protein-histidine kinases
Enzyme Commission (EC)	Acting on ester bonds	0	0.5107	Least Informative	DIRECT
Enzyme Commission (EC)	Protein-histidine kinases	0	1.511	Informative	DIRECT
Enzyme Commission (EC)	Phosphoric diester hydrolases	0	1.379	Informative	DIRECT

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Human Phenotype (HP)

Highlighted in gray are those with FDR_all>0.001

	HP term	FDR (all)	IC level	SDHP level	Annotation (direct or inherited)
Phenotypic Abnormality (PA)	Abnormality of the nervous system	0	0.2371	--	DIRECT
Phenotypic Abnormality (PA)	Abnormality of the vasculature	0	0.7142	--	DIRECT
Phenotypic Abnormality (PA)	Abnormal retinal vascular morphology	0.00005396	2.462	--	DIRECT
Phenotypic Abnormality (PA)	Abnormal visual electrophysiology	0.00006219	2.161	--	DIRECT
Phenotypic Abnormality (PA)	Retinal dystrophy	0.0001217	2.462	--	DIRECT
Phenotypic Abnormality (PA)	Glucose intolerance	0.0006842	1.86	--	DIRECT
Phenotypic Abnormality (PA)	Increased body weight	0.0009945	1.684	--	DIRECT
Phenotypic Abnormality (PA)	Abnormality of the vasculature of the eye	0.001935	1.763	--	INHERITED FROM: Abnormal retinal vascular morphology
Phenotypic Abnormality (PA)	Puberty and gonadal disorders	0.003772	1.207	--	INHERITED FROM: Hypogonadism
Phenotypic Abnormality (PA)	Abnormal retinal morphology	0.005658	1.684	--	INHERITED FROM: Retinal dystrophy || Abnormal retinal vascular morphology || Abnormality of retinal pigmentation
Phenotypic Abnormality (PA)	Abnormal posterior eye segment morphology	0.01566	1.421	--	INHERITED FROM: Abnormal retinal vascular morphology || Abnormality of retinal pigmentation || Retinal dystrophy
Phenotypic Abnormality (PA)	Abnormality of vision	0.0172	1.258	--	INHERITED FROM: Reduced visual acuity
Phenotypic Abnormality (PA)	Abnormality of the genital system	0.03526	0.9309	--	INHERITED FROM: Hypogonadism
Phenotypic Abnormality (PA)	Abnormal eye morphology	0.1078	0.7812	--	INHERITED FROM: Retinal dystrophy || Abnormality of retinal pigmentation || Abnormal retinal vascular morphology
Phenotypic Abnormality (PA)	Growth abnormality	0.1394	0.7903	--	INHERITED FROM: Increased body weight || Obesity
Phenotypic Abnormality (PA)	Abnormality of the cardiovascular system	0	0.5179	Least Informative	DIRECT
Phenotypic Abnormality (PA)	Abnormality of nervous system physiology	0	0.3869	Least Informative	DIRECT
Phenotypic Abnormality (PA)	Abnormality of metabolism/homeostasis	0.1364	0.5486	Least Informative	INHERITED FROM: Glucose intolerance || Diabetes mellitus
Phenotypic Abnormality (PA)	Abnormality of the genitourinary system	0.1387	0.6051	Least Informative	INHERITED FROM: Hypogonadism
Phenotypic Abnormality (PA)	Abnormality of the eye	0.2155	0.5703	Least Informative	INHERITED FROM: Abnormality of retinal pigmentation || Retinal dystrophy || Abnormal electroretinogram || Abnormal retinal vascular morphology || Abnormal visual electrophysiology || Reduced visual acuity
Phenotypic Abnormality (PA)	Behavioral abnormality	0	1.082	Moderately Informative	DIRECT
Phenotypic Abnormality (PA)	Abnormality of the endocrine system	0.02503	0.9183	Moderately Informative	INHERITED FROM: Abnormal circulating hormone level || Hypogonadism || Diabetes mellitus
Phenotypic Abnormality (PA)	Abnormal homeostasis	0.03535	0.7903	Moderately Informative	INHERITED FROM: Glucose intolerance || Diabetes mellitus
Phenotypic Abnormality (PA)	Abnormality of body weight	0.04246	1.12	Moderately Informative	INHERITED FROM: Obesity || Increased body weight
Phenotypic Abnormality (PA)	Abnormal eye physiology	0.1175	0.7903	Moderately Informative	INHERITED FROM: Abnormal electroretinogram || Reduced visual acuity || Abnormal visual electrophysiology
Phenotypic Abnormality (PA)	Obesity	0.0007081	1.684	Informative	DIRECT
Phenotypic Abnormality (PA)	Abnormal circulating hormone level	0.0007176	1.508	Informative	DIRECT
Phenotypic Abnormality (PA)	Abnormality of reproductive system physiology	0.001896	1.508	Informative	INHERITED FROM: Hypogonadism
Phenotypic Abnormality (PA)	Abnormal glucose homeostasis	0.002435	1.383	Informative	INHERITED FROM: Diabetes mellitus || Glucose intolerance
Phenotypic Abnormality (PA)	Visual impairment	0.008624	1.559	Informative	INHERITED FROM: Reduced visual acuity
Phenotypic Abnormality (PA)	Abnormal fundus morphology	0.01543	1.421	Informative	INHERITED FROM: Retinal dystrophy || Abnormality of retinal pigmentation || Abnormal retinal vascular morphology
Phenotypic Abnormality (PA)	Abnormal electroretinogram	0.00003393	2.161	Highly Informative	DIRECT
Phenotypic Abnormality (PA)	Abnormality of retinal pigmentation	0.0001513	2.161	Highly Informative	DIRECT
Phenotypic Abnormality (PA)	Hypogonadism	0.0005727	1.763	Highly Informative	DIRECT
Phenotypic Abnormality (PA)	Diabetes mellitus	0.0006221	1.985	Highly Informative	DIRECT
Phenotypic Abnormality (PA)	Reduced visual acuity	0.0006915	1.985	Highly Informative	DIRECT

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Mouse Phenotype (MP)

Highlighted in gray are those with FDR_all>0.001

	MP term	FDR (all)	IC level	SDMP level	Annotation (direct or inherited)
Mammalian Phenotype (MP)	retinal photoreceptor degeneration	0.000003474	2.302	--	DIRECT
Mammalian Phenotype (MP)	abnormal retinal photoreceptor morphology	0.00004254	1.758	--	DIRECT
Mammalian Phenotype (MP)	abnormal retinal photoreceptor layer morphology	0.00004964	1.758	--	DIRECT
Mammalian Phenotype (MP)	decreased sensory neuron number	0.00007404	1.7	--	DIRECT
Mammalian Phenotype (MP)	neuron degeneration	0.0005052	2.126	--	DIRECT
Mammalian Phenotype (MP)	abnormal retinal layer morphology	0.0008725	1.399	--	DIRECT
Mammalian Phenotype (MP)	abnormal sensory neuron morphology	0.001629	1.156	--	INHERITED FROM: retinal photoreceptor degeneration || abnormal retinal photoreceptor morphology || decreased retinal photoreceptor cell number || decreased sensory neuron number
Mammalian Phenotype (MP)	abnormal neuron number	0.00213	1.399	--	INHERITED FROM: decreased retinal photoreceptor cell number || decreased sensory neuron number
Mammalian Phenotype (MP)	abnormal retina morphology	0.00374	1.241	--	INHERITED FROM: decreased retinal photoreceptor cell number || abnormal retinal photoreceptor layer morphology || abnormal retinal photoreceptor morphology || abnormal retinal neuronal layer morphology || abnormal retinal layer morphology || retinal photoreceptor degeneration
Mammalian Phenotype (MP)	abnormal ocular fundus morphology	0.003848	1.241	--	INHERITED FROM: retinal photoreceptor degeneration || abnormal retinal layer morphology || abnormal retinal neuronal layer morphology || abnormal retinal photoreceptor morphology || abnormal retinal photoreceptor layer morphology || decreased retinal photoreceptor cell number
Mammalian Phenotype (MP)	abnormal posterior eye segment morphology	0.004973	1.223	--	INHERITED FROM: decreased retinal photoreceptor cell number || abnormal retinal photoreceptor layer morphology || abnormal retinal photoreceptor morphology || abnormal retinal neuronal layer morphology || abnormal retinal layer morphology || retinal photoreceptor degeneration
Mammalian Phenotype (MP)	vision/eye phenotype	0.03718	0.8789	--	INHERITED FROM: retinal photoreceptor degeneration || abnormal retinal neuronal layer morphology || decreased retinal photoreceptor cell number || abnormal retinal photoreceptor layer morphology || abnormal eye electrophysiology || abnormal retinal photoreceptor morphology || abnormal retinal layer morphology
Mammalian Phenotype (MP)	abnormal somatic nervous system morphology	0.05678	0.931	--	INHERITED FROM: retinal photoreceptor degeneration || decreased retinal photoreceptor cell number || abnormal retinal photoreceptor morphology || decreased sensory neuron number
Mammalian Phenotype (MP)	abnormal nervous system morphology	0.5142	0.5861	--	INHERITED FROM: abnormal retinal photoreceptor morphology || decreased sensory neuron number || decreased retinal photoreceptor cell number || neuron degeneration || retinal photoreceptor degeneration
Mammalian Phenotype (MP)	nervous system phenotype	0.01376	0.4959	Least Informative	INHERITED FROM: abnormal retinal photoreceptor morphology || decreased retinal photoreceptor cell number || decreased sensory neuron number || retinal photoreceptor degeneration || neuron degeneration
Mammalian Phenotype (MP)	abnormal somatic sensory system morphology	0.004636	1.023	Moderately Informative	INHERITED FROM: abnormal retinal photoreceptor morphology || decreased retinal photoreceptor cell number || retinal photoreceptor degeneration || decreased sensory neuron number
Mammalian Phenotype (MP)	abnormal eye morphology	0.03009	0.9129	Moderately Informative	INHERITED FROM: decreased retinal photoreceptor cell number || abnormal retinal photoreceptor layer morphology || retinal photoreceptor degeneration || abnormal retinal photoreceptor morphology || abnormal retinal neuronal layer morphology || abnormal retinal layer morphology
Mammalian Phenotype (MP)	abnormal neuron morphology	0.2334	0.8323	Moderately Informative	INHERITED FROM: neuron degeneration || decreased sensory neuron number || retinal photoreceptor degeneration || abnormal retinal photoreceptor morphology || decreased retinal photoreceptor cell number
Mammalian Phenotype (MP)	abnormal retinal neuronal layer morphology	0.0004156	1.427	Informative	DIRECT
Mammalian Phenotype (MP)	decreased neuron number	0.001108	1.562	Informative	INHERITED FROM: decreased sensory neuron number || decreased retinal photoreceptor cell number
Mammalian Phenotype (MP)	abnormal eye physiology	0.001387	1.649	Informative	INHERITED FROM: abnormal eye electrophysiology
Mammalian Phenotype (MP)	decreased retinal photoreceptor cell number	0.000002457	2.001	Highly Informative	DIRECT
Mammalian Phenotype (MP)	abnormal eye electrophysiology	0.00007914	2.001	Highly Informative	DIRECT
Mammalian Phenotype (MP)	neurodegeneration	0.006267	2.001	Highly Informative	INHERITED FROM: neuron degeneration || retinal photoreceptor degeneration

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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)	anatomical structure	0	0	--	DIRECT
Xenopus DEvelopment stage (XDE)	NF stage	0	0.01895	--	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)	whole plant	0	0.3507	--	DIRECT
Plant ANatomical entity (PAN)	cauline leaf	0	0.6042	--	DIRECT
Plant ANatomical entity (PAN)	inflorescence meristem	0	0.6337	--	DIRECT
Plant ANatomical entity (PAN)	phyllome	0	0.3234	--	DIRECT
Plant ANatomical entity (PAN)	leaf lamina base	0	0.6245	--	DIRECT
Plant ANatomical entity (PAN)	shoot system	0	0.05272	--	DIRECT
Plant ANatomical entity (PAN)	portion of plant tissue	0	0.1621	--	DIRECT
Plant ANatomical entity (PAN)	plant organ	0	0.2391	--	DIRECT
Plant ANatomical entity (PAN)	sporophyll	0	0.3985	--	DIRECT
Plant ANatomical entity (PAN)	stamen	0	0.5171	--	DIRECT
Plant ANatomical entity (PAN)	carpel	0	0.5117	--	DIRECT
Plant ANatomical entity (PAN)	flower	0	0.3446	--	DIRECT
Plant ANatomical entity (PAN)	pedicel	0	0.5373	--	DIRECT
Plant ANatomical entity (PAN)	perianth	0	0.4476	--	DIRECT
Plant ANatomical entity (PAN)	corolla	0	0.4893	--	DIRECT
Plant ANatomical entity (PAN)	calyx	0	0.4728	--	DIRECT
Plant ANatomical entity (PAN)	inflorescence branch	0	0.5373	--	DIRECT
Plant ANatomical entity (PAN)	petiole	0	0.6385	--	DIRECT
Plant ANatomical entity (PAN)	inflorescence axis	0	0.5373	--	DIRECT
Plant ANatomical entity (PAN)	leaf apex	0	0.5999	--	DIRECT
Plant ANatomical entity (PAN)	stem internode	0	0.5373	--	DIRECT
Plant ANatomical entity (PAN)	cardinal organ part	0	0.4385	--	DIRECT
Plant ANatomical entity (PAN)	plant axis	0	0.3257	--	DIRECT
Plant ANatomical entity (PAN)	collective phyllome structure	0	0.3837	--	DIRECT
Plant ANatomical entity (PAN)	root system	0	0.4584	--	DIRECT
Plant ANatomical entity (PAN)	shoot axis	0	0.3985	--	DIRECT
Plant ANatomical entity (PAN)	leaf	0	0.4282	--	DIRECT
Plant ANatomical entity (PAN)	lamina	0	0.6199	--	DIRECT
Plant ANatomical entity (PAN)	reproductive shoot system	0	0.3304	--	DIRECT
Plant ANatomical entity (PAN)	multi-tissue plant structure	0	0.2335	--	DIRECT
Plant ANatomical entity (PAN)	collective plant structure	0	0.01555	--	DIRECT
Plant ANatomical entity (PAN)	cardinal part of multi-tissue plant structure	0	0.437	--	DIRECT
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 || cardinal organ part || multi-tissue plant structure || microsporophyll || megasporophyll || cauline leaf || reproductive shoot system || shoot apex || leaf apex || leaf lamina base || branch || collective leaf structure || stem internode || inflorescence branch || shoot system || portion of plant tissue || plant organ || portion of meristem tissue || stem || whole plant || inflorescence meristem || root system || inflorescence || cardinal part of multi-tissue plant structure || petiole || stalk || gynoecium || vascular leaf || sepal || fruit || leaf lamina || corolla || plant axis || collective phyllome structure || petal || carpel || seed || phyllome apex || stamen || shoot axis || pedicel || androecium
Plant ANatomical entity (PAN)	collective plant organ structure	1	0.03998	--	INHERITED FROM: inflorescence axis || calyx || flower || sporophyll || inflorescence meristem || 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 || megasporophyll || cauline leaf || microsporophyll || leaf lamina || corolla || pedicel || androecium || phyllome apex || stamen || stem internode || inflorescence branch || shoot axis || shoot system || leaf lamina base || collective leaf structure || branch
Plant ANatomical entity (PAN)	phyllome lamina	1	0.6199	--	INHERITED FROM: leaf lamina base || leaf lamina
Plant ANatomical entity (PAN)	organ lamina	1	0.6199	--	INHERITED FROM: leaf lamina base || leaf lamina
Plant ANatomical entity (PAN)	shoot apex	0	0.481	Least Informative	DIRECT
Plant ANatomical entity (PAN)	shoot internode	0	0.5373	Least Informative	DIRECT
Plant ANatomical entity (PAN)	root	0	0.4679	Least Informative	DIRECT
Plant ANatomical entity (PAN)	plant embryo	0	0.4978	Least Informative	DIRECT
Plant ANatomical entity (PAN)	seed	0	0.5189	Least Informative	DIRECT
Plant ANatomical entity (PAN)	portion of meristem tissue	0	0.5892	Least Informative	DIRECT
Plant ANatomical entity (PAN)	vascular leaf	0	0.437	Least Informative	DIRECT
Plant ANatomical entity (PAN)	megasporophyll	0	0.5117	Least Informative	DIRECT
Plant ANatomical entity (PAN)	microsporophyll	0	0.4415	Least Informative	DIRECT
Plant ANatomical entity (PAN)	sepal	0	0.4728	Least Informative	DIRECT
Plant ANatomical entity (PAN)	petal	0	0.4893	Least Informative	DIRECT
Plant ANatomical entity (PAN)	stem	0	0.4777	Least Informative	DIRECT
Plant ANatomical entity (PAN)	inflorescence	0	0.4859	Least Informative	DIRECT
Plant ANatomical entity (PAN)	androecium	0	0.5153	Least Informative	DIRECT
Plant ANatomical entity (PAN)	gynoecium	0	0.5082	Least Informative	DIRECT
Plant ANatomical entity (PAN)	leaf lamina	0	0.6199	Least Informative	DIRECT
Plant ANatomical entity (PAN)	collective leaf structure	0	0.46	Least Informative	DIRECT
Plant ANatomical entity (PAN)	stalk	0	0.6176	Least Informative	DIRECT
Plant ANatomical entity (PAN)	branch	0	0.5373	Least Informative	DIRECT
Plant ANatomical entity (PAN)	phyllome apex	0	0.5956	Least Informative	DIRECT
Plant ANatomical entity (PAN)	fruit	0.0001402	1.345	Informative	DIRECT
Plant structure DEvelopment stage (PDE)	whole plant development stage	0	0.1547	--	DIRECT
Plant structure DEvelopment stage (PDE)	sporophyte vegetative stage	0	0.1593	--	DIRECT
Plant structure DEvelopment stage (PDE)	floral organ differentiation stage	0	0.07163	--	DIRECT
Plant structure DEvelopment stage (PDE)	corolla development stage	0	0.1484	--	DIRECT
Plant structure DEvelopment stage (PDE)	flowering stage	0	0.1648	--	DIRECT
Plant structure DEvelopment stage (PDE)	plant embryo stage	0	0.2319	--	DIRECT
Plant structure DEvelopment stage (PDE)	collective plant organ structure development stage	0	0.0282	--	DIRECT
Plant structure DEvelopment stage (PDE)	plant organ development stage	0	0.06127	--	DIRECT
Plant structure DEvelopment stage (PDE)	reproductive shoot system development stage	0	0.0371	--	DIRECT
Plant structure DEvelopment stage (PDE)	collective phyllome structure development stage	0	0.07163	--	DIRECT
Plant structure DEvelopment stage (PDE)	phyllome development stage	0	0.3879	--	DIRECT
Plant structure DEvelopment stage (PDE)	floral organ formation stage	0	0.07163	--	DIRECT
Plant structure DEvelopment stage (PDE)	leaf development stage	1	0.3879	--	INHERITED FROM: 4 leaf senescence stage
Plant structure DEvelopment stage (PDE)	flower development stage	1	0.05402	--	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	0.1584	--	INHERITED FROM: sporophyte vegetative stage || C globular stage || E expanded cotyledon stage || F mature embryo stage || D bilateral stage || plant embryo stage || seedling development stage
Plant structure DEvelopment stage (PDE)	shoot system development stage	1	0.02956	--	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)	sporophyte development stage	1	0.1584	--	INHERITED FROM: E expanded cotyledon stage || sporophyte vegetative stage || C globular stage || seedling development stage || D bilateral stage || F mature embryo stage || plant embryo stage
Plant structure DEvelopment stage (PDE)	4 leaf senescence stage	0	0.3895	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	E expanded cotyledon stage	0	0.2861	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	F mature embryo stage	0	0.3205	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	C globular stage	0	0.3087	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	D bilateral stage	0	0.301	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	seedling development stage	0.000003318	1.721	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)	3',5'-cyclic-GMP phosphodiesterase	0	2.929	--	DIRECT
Enzyme Commission (EC)	Transferring phosphorus-containing groups	0.00000000004937	0.7021	--	DIRECT
Enzyme Commission (EC)	Hydrolases	0.00000000001962	0.4043	Least Informative	DIRECT
Enzyme Commission (EC)	Transferases	0.03783	0.3972	Least Informative	INHERITED FROM: Protein-histidine kinases || Transferring phosphorus-containing groups
Enzyme Commission (EC)	Acting on ester bonds	0	0.8756	Moderately Informative	DIRECT
Enzyme Commission (EC)	Protein-histidine kinases	0	1.974	Highly Informative	DIRECT
Enzyme Commission (EC)	Phosphoric diester hydrolases	0	1.753	Highly Informative	DIRECT

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