SUPERFAMILY 1.75 HMM library and genome assignments server

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RUN domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   RUN domain-like [ 140740]
Superfamily:   RUN domain-like [ 140741]
Families:   RUN domain [ 140742]

 Superfamily statistics
Genomes (148) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 2,201 2,010 1
Proteins 1,995 1,830 1

 Functional annotation
General category Regulation
Detailed category Signal transduction

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 0.8268 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.9777 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) signal transduction 0.5417 Moderately Informative Inherited
Biological Process (BP) intracellular signal transduction 0.01235 Informative Inherited
Biological Process (BP) small GTPase mediated signal transduction 5.662e-06 Highly Informative Direct
Molecular Function (MF) binding 0.6539 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 7.844e-07 Moderately Informative Direct
Molecular Function (MF) protein binding 0.1034 Moderately Informative Inherited
Molecular Function (MF) GTPase regulator activity 1.03e-07 Informative Direct
Molecular Function (MF) enzyme binding 0.003282 Informative Inherited
Molecular Function (MF) small GTPase regulator activity 2.941e-09 Highly Informative Direct
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.08629 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) endosome 2.382e-06 Informative Direct

Document: GO annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)male genitalia0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentEndosome3.099e-12Moderately InformativeDirect
Cellular componentGolgi apparatus1.467e-05Moderately InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
DomainSH3 domain3.153e-12InformativeDirect
Molecular functionZinc0.0006731Least InformativeDirect
Molecular functionMetal-binding0.6909Least InformativeInherited
Molecular functionZinc-finger1.63e-08Moderately InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor2.728e-10InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · 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 1 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 RUN domain-like 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 1 hidden Markov models representing the RUN domain-like 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) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · 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.

Please send feedback, comments or questions to superfamily@cs.bris.ac.uk or use the feedback form.

© Copyright 2013 The SUPERFAMILY authors and Julian Gough.