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 (1,427) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,820 7,695 3
Proteins 3,814 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) cellular macromolecule metabolic process 0.3781 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.02614 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.05857 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.01186 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.01387 Least Informative Inherited
Biological Process (BP) cellular catabolic process 0.02188 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.07234 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.131 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.08222 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.09608 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.1058 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.0439 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.0352 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.5602 Moderately Informative Inherited
Biological Process (BP) nucleoside monophosphate metabolic process 0.0004667 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.000781 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.002693 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.003274 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.001651 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.01732 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.003533 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.002029 Informative Inherited
Biological Process (BP) response to heat 0.00001218 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 0.00009424 Highly Informative Direct
Biological Process (BP) ribonucleoside triphosphate catabolic process 0.0005508 Highly Informative Direct
Biological Process (BP) purine nucleoside triphosphate catabolic process 0.0005802 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0.0006958 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0.0007508 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.04026 Least Informative Inherited
Molecular Function (MF) binding 0.879 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0008475 Moderately Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 0.00001313 Informative Direct
Molecular Function (MF) RNA binding 0.0005961 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 an0.000000002996Moderately 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 anhydrides0.03104Moderately InformativeInherited
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)RNA helicase0.000000000005674InformativeDirect
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 regulation0.0000001118Moderately InformativeDirect
Biological processmRNA splicing0.00000000002818InformativeDirect
Cellular componentNucleus0Least InformativeDirect
DomainZinc-finger0.00000003174Moderately InformativeDirect
Molecular functionDNA-binding0.00009031Least InformativeDirect
Molecular functionZinc0.0006651Least InformativeDirect
Molecular functionRNA-binding0.000003513Moderately InformativeDirect
Post-translational modificationHydrolase0.0108Least InformativeInherited
Post-translational modificationActivator0.00007698Moderately InformativeDirect
Post-translational modificationRepressor0.0001295Moderately InformativeDirect
Post-translational modificationNuclease0.0002117Moderately InformativeDirect
Post-translational modificationExonuclease0.0000000002794InformativeDirect
Post-translational modificationHelicase0.00005483InformativeDirect
Post-translational modificationPhosphoprotein0.00000000526Least 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 ]