SUPERFAMILY 1.75 HMM library and genome assignments server

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Release factor superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   Release factor [ 75619]
Superfamily:   Release factor [ 75620]
Families:   Release factor [ 75621] (2)

Superfamily statistics
Genomes (2,341) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 5,955 18,397 5
Proteins 5,934 18,383 5

 Functional annotation
General category Information
Detailed category Translation

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)biosynthetic process0.00038393.425e-05Least InformativeDirect
Biological Process (BP)protein metabolic process0.00058856.923e-05Least InformativeDirect
Biological Process (BP)single-organism cellular process0.1970.2481Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.0031170.001393Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.0049210.002257Least InformativeInherited
Biological Process (BP)gene expression7.795e-077.721e-06Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process3.931e-062.611e-06Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.0020711.218e-06Moderately InformativeInherited
Biological Process (BP)cellular component disassembly1.401e-092.076e-15InformativeDirect
Biological Process (BP)cellular protein complex disassembly10Highly InformativeInherited
Molecular Function (MF)binding0.38570.404Least InformativeInherited
Molecular Function (MF)organic cyclic compound binding0.0041140.0003287Moderately InformativeInherited
Molecular Function (MF)heterocyclic compound binding0.0032950.0002853Moderately InformativeInherited
Molecular Function (MF)RNA binding5.378e-062.493e-09InformativeDirect
Molecular Function (MF)translation factor activity, nucleic acid binding2.199e-091.036e-07Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biosynthetic process 3.425e-05 Least Informative Direct
Biological Process (BP) protein metabolic process 6.923e-05 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.2481 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.001393 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.002257 Least Informative Inherited
Biological Process (BP) gene expression 7.721e-06 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 2.611e-06 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 1.218e-06 Moderately Informative Direct
Biological Process (BP) cellular component disassembly 2.076e-15 Informative Direct
Biological Process (BP) cellular protein complex disassembly 0 Highly Informative Direct
Molecular Function (MF) binding 0.404 Least Informative Inherited
Molecular Function (MF) organic cyclic compound binding 0.0003287 Moderately Informative Direct
Molecular Function (MF) heterocyclic compound binding 0.0002853 Moderately Informative Direct
Molecular Function (MF) RNA binding 2.493e-09 Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 1.036e-07 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0005951 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1.552e-05 Least Informative Direct
Cellular Component (CC) plastid 1.968e-06 Informative Direct

Document: GO annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)vascular leaf0Least InformativeDirect
Plant ANatomical entity (PAN)stalk0Least InformativeDirect
Plant ANatomical entity (PAN)petal0Least InformativeDirect
Plant ANatomical entity (PAN)sepal0Least InformativeDirect
Plant ANatomical entity (PAN)pedicel0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least InformativeDirect
Plant ANatomical entity (PAN)plant embryo0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)phyllome apex0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)stem0Least InformativeDirect
Plant ANatomical entity (PAN)leaf lamina0Least InformativeDirect
Plant ANatomical entity (PAN)shoot internode0Least InformativeDirect
Plant ANatomical entity (PAN)shoot apex0Least InformativeDirect
Plant ANatomical entity (PAN)androecium0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon 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)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentCytoplasm0Least InformativeDirect
Coding sequence diversityRibosomal frameshifting0Moderately InformativeDirect
Post-translational modificationMethylation0Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Arabidopsis Plant Ontology (AP) · 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 Release factor 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 Release factor 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-quality) · Gene Ontology (high-coverage) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.