SUPERFAMILY 1.75 HMM library and genome assignments server

  Home > SCOP hierarchy > BEACH domain superfamily


BEACH domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   BEACH domain [ 81836]
Superfamily:   BEACH domain [ 81837]
Families:   BEACH domain [ 81838] (2)

Superfamily statistics
Genomes (418) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 1,982 1,720 2
Proteins 1,951 1,705 2

 Functional annotation
General category Other
Detailed category Unknown function

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) localization 0.0003989 Least Informative Direct
Biological Process (BP) response to stimulus 0.05076 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.02694 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.009715 Least Informative Inherited
Biological Process (BP) immune system process 7.386e-05 Moderately Informative Direct
Biological Process (BP) cellular localization 2.961e-08 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.06585 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.06711 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.3337 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.1809 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.6782 Moderately Informative Inherited
Biological Process (BP) immune effector process 0.0008117 Informative Direct
Biological Process (BP) immune response 0.000961 Informative Direct
Biological Process (BP) protein transport 0.0002537 Informative Direct
Biological Process (BP) response to external stimulus 0.01732 Informative Inherited
Biological Process (BP) cellular component movement 0.03141 Informative Inherited
Biological Process (BP) localization of cell 0.06991 Informative Inherited
Biological Process (BP) locomotion 0.02194 Informative Inherited
Biological Process (BP) defense response 0.001123 Informative Inherited
Biological Process (BP) secretion 0.03195 Informative Inherited
Biological Process (BP) response to other organism 0.006836 Informative Inherited
Biological Process (BP) leukocyte mediated immunity 8.177e-10 Highly Informative Direct
Biological Process (BP) chemotaxis 0.0008496 Highly Informative Direct
Biological Process (BP) response to virus 1.841e-06 Highly Informative Direct
Biological Process (BP) vesicle organization 1.072e-10 Highly Informative Direct
Biological Process (BP) endosomal transport 1.826e-08 Highly Informative Direct
Biological Process (BP) leukocyte migration 4.21e-05 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.1673 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.9805 Least Informative Inherited
Cellular Component (CC) vesicle 7.508e-05 Moderately Informative Direct
Cellular Component (CC) vacuole 0.0003783 Informative Direct

Document: GO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of head and neck0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.02678Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of thrombocytes0.0003604InformativeDirect
Phenotypic Abnormality (PA)Thrombocytopenia0.0001436Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0Least InformativeDirect
Mammalian Phenotype (MP)integument phenotype0Moderately InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentMembrane5.982e-05Least InformativeDirect
Cellular componentEndoplasmic reticulum4.876e-06Moderately InformativeDirect
Coding sequence diversityAlternative splicing0Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainWD repeat0InformativeDirect
Post-translational modificationPhosphoprotein1.038e-08Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000409 SSF81837 Protein matches
Abstract

The "beige" mouse is established as an animal model of Chediak-Higashi Syndrome (CHS) [PubMed8896560]. The BEACH domain was described in the BEIGE protein (D1035670) and in the highly homologous CHS protein . It is also found in distantly related proteins like, for example, and which are factor associated with neutral sphingomyelinase activation [PubMed9620659].

The BEACH domain is usually followed by a series of WD repeats . The function of the BEACH domain is unknown.


InterPro database

PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · 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 2 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 BEACH 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 2 hidden Markov models representing the BEACH 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · 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.

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.