SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (1,435) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 3,890 14,568 3
Proteins 3,884 14,548 3

Functional annotation
General category Regulation
Detailed category RNA binding, metabolism and transport

Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Molecular Function (MF) hydrolase activity 0.02196 Least Informative Inherited
Molecular Function (MF) binding 0.3247 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0000001868 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.00001463 Moderately Informative Direct
Molecular Function (MF) catalytic activity, acting on RNA 0.0002625 Moderately Informative Direct
Molecular Function (MF) RNA binding 0.0000005247 Informative Direct
Molecular Function (MF) catalytic activity, acting on DNA 0.000002816 Informative Direct
Molecular Function (MF) ATPase activity 0.8325 Informative Inherited

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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0.0000002766Moderately InformativeDirect
Biological processmRNA processing0.000000009809InformativeDirect
Cellular componentNucleus0Least InformativeDirect
DomainZinc-finger0.00000005137Moderately InformativeDirect
Post-translational modificationHydrolase0.003072Least InformativeInherited
Post-translational modificationRNA-binding0.0000005814Moderately InformativeDirect
Post-translational modificationDNA-binding0.00003017Moderately InformativeDirect
Post-translational modificationActivator0.0001353Moderately InformativeDirect
Post-translational modificationRepressor0.0002187Moderately InformativeDirect
Post-translational modificationNuclease0.0005876Moderately InformativeDirect
Post-translational modificationExonuclease0.0000000004011InformativeDirect
Post-translational modificationHelicase0.0000009489InformativeDirect
Post-translational modificationPhosphoprotein0.0000000000009957Least InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · 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) · UniProtKB KeyWords (KW) · Internal database links ]