R3H domain superfamily

SCOP classification

Root:	SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:	Alpha and beta proteins (a+b) [ 53931] (376)
Fold:	IF3-like [ 55199] (8)
Superfamily:	R3H domain [ 82708]
Families:	R3H domain [ 82709] (3)

Superfamily statistics

	Genomes (1,118)	Uniprot 2013_05	PDB chains (SCOP 1.75)
Domains	3,211	4,736	3
Proteins	3,208	4,734	3

Functional annotation

General category	Regulation
Detailed category	RNA binding, metabolism and transport

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)	single-organism cellular process	1	Least Informative	Inherited
Biological Process (BP)	response to stimulus	1	Least Informative	Inherited
Biological Process (BP)	cellular response to stress	0.02342	Moderately Informative	Inherited
Biological Process (BP)	response to abiotic stimulus	0.05466	Moderately Informative	Inherited
Biological Process (BP)	response to heat	3.23e-06	Highly Informative	Direct
Molecular Function (MF)	hydrolase activity	0.02841	Least Informative	Inherited
Molecular Function (MF)	nucleoside-triphosphatase activity	2.311e-05	Informative	Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Acting on acid anhydrides	0.03241	Least Informative	Inherited
Enzyme Commission (EC)	Acting on ester bonds	0.03192	Least Informative	Inherited
Enzyme Commission (EC)	Acting on acid anhydrides; involved in cellular an	2.996e-09	Moderately Informative	Direct
Enzyme Commission (EC)	Poly(A)-specific ribonuclease	0	Highly Informative	Direct

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)

	WP term	FDR (all)	SDWP level	Annotation (direct or inherited)
Worm Phenotype (WP)	growth variant	0	Least Informative	Direct
Worm Phenotype (WP)	developmental timing variant	0	Least Informative	Direct
Worm Phenotype (WP)	larval development variant	0	Least Informative	Direct
Worm Phenotype (WP)	larval lethal	0	Moderately Informative	Direct
Worm Phenotype (WP)	sterile progeny	0	Moderately Informative	Direct

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)

	YP term	FDR (all)	SDYP level	Annotation (direct or inherited)
Yeast Phenotype (YP)	resistance to chemicals	0	Least Informative	Direct

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)

	XA term	FDR (all)	SDXA level	Annotation (direct or inherited)
Xenopus ANatomical entity (XAN)	male genitalia	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	head	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	gonad	0	Least Informative	Direct

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)

	AP term	FDR (all)	SDAP level	Annotation (direct or inherited)
Plant ANatomical entity (PAN)	shoot apex	0	Least Informative	Direct
Plant ANatomical entity (PAN)	shoot internode	0	Least Informative	Direct
Plant ANatomical entity (PAN)	root	0	Least Informative	Direct
Plant ANatomical entity (PAN)	plant embryo	0	Least Informative	Direct
Plant ANatomical entity (PAN)	seed	0	Least Informative	Direct
Plant ANatomical entity (PAN)	portion of meristem tissue	0	Least Informative	Direct
Plant ANatomical entity (PAN)	vascular leaf	0	Least Informative	Direct
Plant ANatomical entity (PAN)	megasporophyll	0	Least Informative	Direct
Plant ANatomical entity (PAN)	microsporophyll	0	Least Informative	Direct
Plant ANatomical entity (PAN)	sepal	0	Least Informative	Direct
Plant ANatomical entity (PAN)	petal	0	Least Informative	Direct
Plant ANatomical entity (PAN)	stem	0	Least Informative	Direct
Plant ANatomical entity (PAN)	pedicel	0	Least Informative	Direct
Plant ANatomical entity (PAN)	androecium	0	Least Informative	Direct
Plant ANatomical entity (PAN)	gynoecium	0	Least Informative	Direct
Plant ANatomical entity (PAN)	leaf lamina	0	Least Informative	Direct
Plant ANatomical entity (PAN)	collective leaf structure	0	Least Informative	Direct
Plant ANatomical entity (PAN)	stalk	0	Least Informative	Direct
Plant ANatomical entity (PAN)	phyllome apex	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	4 leaf senescence stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	E expanded cotyledon stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	F mature embryo stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	C globular stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	D bilateral stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	LP.12 twelve leaves visible stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	LP.08 eight leaves visible stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	LP.02 two leaves visible stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	LP.10 ten leaves visible stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	LP.04 four leaves visible stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	LP.06 six leaves visible stage	0	Least Informative	Direct

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Hydrolases	0	Least Informative	Direct
Enzyme Commission (EC)	Acting on acid anhydrides	0.03211	Moderately Informative	Inherited
Enzyme Commission (EC)	Exoribonucleases producing 5'-phosphomonoesters	0	Informative	Direct
Enzyme Commission (EC)	RNA helicase	6.419e-12	Informative	Direct
Enzyme Commission (EC)	Poly(A)-specific ribonuclease	0	Highly Informative	Direct

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)

	KW term	FDR (all)	SDKW level	Annotation (direct or inherited)
Biological process	Transcription regulation	7.705e-08	Moderately Informative	Direct
Biological process	mRNA splicing	2.388e-11	Informative	Direct
Cellular component	Nucleus	0	Least Informative	Direct
Molecular function	Zinc	0.0005549	Least Informative	Direct
Molecular function	Metal-binding	0.02197	Least Informative	Inherited
Molecular function	Nucleotide-binding	1	Least Informative	Inherited
Molecular function	Zinc-finger	1.675e-07	Moderately Informative	Direct
Molecular function	RNA-binding	6.243e-05	Moderately Informative	Direct
Molecular function	DNA-binding	6.935e-05	Moderately Informative	Direct
Molecular function	Helicase	3.81e-06	Informative	Direct
Post-translational modification	Hydrolase	0.009655	Least Informative	Inherited
Post-translational modification	Activator	7.282e-05	Moderately Informative	Direct
Post-translational modification	Repressor	0.0001144	Moderately Informative	Direct
Post-translational modification	Nuclease	0.0001885	Moderately Informative	Direct
Post-translational modification	Exonuclease	2.486e-10	Informative	Direct
Post-translational modification	Phosphoprotein	1.664e-12	Least Informative	Direct

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · 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 3 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 R3H 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 3 hidden Markov models representing the R3H domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.

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R3H domain superfamily