SUPERFAMILY 1.75 HMM library and genome assignments server


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 (1,425) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,797 7,695 3
Proteins 3,792 7,692 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) cellular macromolecule metabolic process 0.3344 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.008331 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.01902 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.009775 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.04368 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.932 Least Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.0004433 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.06249 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.1165 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.0757 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.05321 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.4759 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.06547 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.0182 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.01897 Moderately Informative Inherited
Biological Process (BP) nucleoside monophosphate metabolic process 0.0002369 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 0.0009289 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.0008699 Informative Direct
Biological Process (BP) DNA metabolic process 0.005906 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.002161 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.003582 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.00224 Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0.001606 Informative Inherited
Biological Process (BP) glycosyl compound catabolic process 0.0037 Informative Inherited
Biological Process (BP) nucleoside monophosphate catabolic process 8.77e-05 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0.0006546 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate catabolic process 0.0004793 Highly Informative Direct
Biological Process (BP) response to heat 1.065e-05 Highly Informative Direct
Biological Process (BP) ATP metabolic process 0.0001134 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0.0006066 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.03391 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 1.979e-05 Moderately Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 1.06e-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)Acting on acid anhydrides0.03241Least InformativeInherited
Enzyme Commission (EC)Acting on ester bonds0.03192Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an2.996e-09Moderately InformativeDirect
Enzyme Commission (EC)Poly(A)-specific ribonuclease0Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)late embryo0Moderately InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible 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)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.03125Moderately InformativeInherited
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)RNA helicase5.741e-12InformativeDirect
Enzyme Commission (EC)Poly(A)-specific ribonuclease0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation1.092e-07Moderately InformativeDirect
Biological processmRNA splicing2.758e-11InformativeDirect
Cellular componentNucleus0Least InformativeDirect
DomainZinc-finger3.2e-08Moderately InformativeDirect
Molecular functionZinc0.0006267Least InformativeDirect
Molecular functionRNA-binding3.474e-06Moderately InformativeDirect
Molecular functionDNA-binding9.059e-05Moderately InformativeDirect
Post-translational modificationHydrolase0.01053Least InformativeInherited
Post-translational modificationActivator7.688e-05Moderately InformativeDirect
Post-translational modificationRepressor0.0001222Moderately InformativeDirect
Post-translational modificationNuclease0.0002155Moderately InformativeDirect
Post-translational modificationExonuclease2.801e-10InformativeDirect
Post-translational modificationHelicase5.506e-05InformativeDirect
Post-translational modificationPhosphoprotein5.123e-09Least InformativeDirect

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) · Fly Anatomy (FA) · 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.


Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]