SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (473) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,296 2,406 2
Proteins 2,262 2,384 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) single-organism cellular process 0.09075 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.001584 Least Informative Inherited
Biological Process (BP) response to stimulus 0.01498 Least Informative Inherited
Biological Process (BP) immune system process 0.00002309 Moderately Informative Direct
Biological Process (BP) cellular developmental process 0.08609 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.5231 Moderately Informative Inherited
Biological Process (BP) immune response 0.00005479 Informative Direct
Biological Process (BP) cell development 0.0005373 Informative Direct
Biological Process (BP) vesicle organization 0.00000002081 Highly Informative Direct
Biological Process (BP) endosomal transport 0.0000485 Highly Informative Direct
Biological Process (BP) pigmentation 0.0000001349 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.979 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.08864 Least Informative Inherited
Cellular Component (CC) vacuole 0.00001304 Moderately Informative Direct

Document: GO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Pace of progression0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the face0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the integument0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.1178Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.1607Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.02354Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.0342Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the gastrointestinal tract0.03444Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digestive system physiology0.03456Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin morphology0.08418Moderately InformativeInherited
Phenotypic Abnormality (PA)Functional abnormality of the gastrointestinal tract0.0004603InformativeDirect
Phenotypic Abnormality (PA)Vascular skin abnormality0.001694InformativeInherited
Phenotypic Abnormality (PA)Subcutaneous hemorrhage0.0001819Highly InformativeDirect
Phenotypic Abnormality (PA)Thrombocytopenia0.0003583Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP 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)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)brain0Moderately InformativeDirect

Document: XA 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 componentMembrane0.0005688Least InformativeDirect
Cellular componentEndoplasmic reticulum0.00002099Moderately InformativeDirect
Coding sequence diversityAlternative splicing0.00000000000001117Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainWD repeat0InformativeDirect
Post-translational modificationPhosphoprotein0.00003951Least 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) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · 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) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]