SUPERFAMILY 1.75 HMM library and genome assignments server

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 (472) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,295 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) response to stimulus 0.0001143 Least Informative Direct
Biological Process (BP) localization 0.0004399 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.000207 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.07538 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.1623 Least Informative Inherited
Biological Process (BP) developmental process 0.3861 Least Informative Inherited
Biological Process (BP) immune system process 0.00000001362 Moderately Informative Direct
Biological Process (BP) cellular localization 0.00003857 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.511 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.1337 Moderately Informative Inherited
Biological Process (BP) organ development 0.006706 Moderately Informative Inherited
Biological Process (BP) defense response 0.1511 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.01946 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.4262 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.005669 Moderately Informative Inherited
Biological Process (BP) response to bacterium 0.0006714 Informative Direct
Biological Process (BP) response to nutrient levels 0.0008456 Informative Direct
Biological Process (BP) secretion by cell 0.0006043 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.000001012 Informative Direct
Biological Process (BP) regulation of body fluid levels 0.00000000002053 Informative Direct
Biological Process (BP) cellular component movement 0.03421 Informative Inherited
Biological Process (BP) defense response to other organism 0.04872 Informative Inherited
Biological Process (BP) immune effector process 0.009095 Informative Inherited
Biological Process (BP) localization of cell 0.03646 Informative Inherited
Biological Process (BP) single-organism intracellular transport 0.002157 Informative Inherited
Biological Process (BP) locomotion 0.01326 Informative Inherited
Biological Process (BP) chemotaxis 0.0001483 Highly Informative Direct
Biological Process (BP) hemostasis 0.00000000000003411 Highly Informative Direct
Biological Process (BP) response to virus 0.000002033 Highly Informative Direct
Biological Process (BP) vesicle organization 0 Highly Informative Direct
Biological Process (BP) wound healing 0.0000000000195 Highly Informative Direct
Biological Process (BP) defense response to bacterium 0.00003067 Highly Informative Direct
Biological Process (BP) coagulation 0.00000000000008678 Highly Informative Direct
Biological Process (BP) leukocyte migration 0.0001104 Highly Informative Direct
Biological Process (BP) myeloid cell development 0.000000006109 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.001498 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.09943 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.9433 Least Informative Inherited
Cellular Component (CC) vesicle 0.003121 Moderately Informative Inherited

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 tissues0.02673Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of thrombocytes0.0003465InformativeDirect
Phenotypic Abnormality (PA)Thrombocytopenia0.0001435Highly 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

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 componentMembrane0.00006437Least InformativeDirect
Cellular componentEndoplasmic reticulum0.000006249Moderately InformativeDirect
Coding sequence diversityAlternative splicing0.000000000000004395Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainWD repeat0InformativeDirect
Post-translational modificationPhosphoprotein0.00002766Least 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 ]