SUPERFAMILY 1.75 HMM library and genome assignments server


Subdomain of clathrin and coatomer appendage domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Subdomain of clathrin and coatomer appendage domain [ 55710]
Superfamily:   Subdomain of clathrin and coatomer appendage domain [ 55711] (2)
Families:   Clathrin adaptor appendage, alpha and beta chain-specific domain [ 55712] (2)
  Coatomer appendage domain [ 103159]


Superfamily statistics
Genomes (441) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 1,550 1,330 7
Proteins 1,550 1,330 7


Functional annotation
General category Processes_IC
Detailed category Transport

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 2.503e-05 Least Informative Direct
Biological Process (BP) localization 0 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.1115 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.0197 Least Informative Inherited
Biological Process (BP) system process 3.693e-05 Moderately Informative Direct
Biological Process (BP) cellular localization 3.746e-15 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.004004 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.1127 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.6081 Moderately Informative Inherited
Biological Process (BP) cell-cell signaling 6.688e-07 Informative Direct
Biological Process (BP) protein transport 0 Informative Direct
Biological Process (BP) vesicle-mediated transport 1.431e-14 Informative Direct
Biological Process (BP) transmission of nerve impulse 8.638e-08 Informative Direct
Biological Process (BP) membrane organization 1.577e-06 Informative Direct
Biological Process (BP) organelle localization 0.1855 Informative Inherited
Biological Process (BP) vesicle organization 1.534e-11 Highly Informative Direct
Biological Process (BP) establishment of vesicle localization 0.007998 Highly Informative Inherited
Biological Process (BP) synaptic vesicle localization 0.1129 Highly Informative Inherited
Molecular Function (MF) binding 0.003115 Least Informative Inherited
Molecular Function (MF) transporter activity 0.0006279 Moderately Informative Direct
Molecular Function (MF) protein transporter activity 5.673e-10 Highly Informative Direct
Cellular Component (CC) membrane 5.839e-15 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 9.238e-09 Least Informative Direct
Cellular Component (CC) protein complex 7.025e-09 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.4456 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.001235 Least Informative Inherited
Cellular Component (CC) endomembrane system 2.997e-13 Moderately Informative Direct
Cellular Component (CC) organelle membrane 2.625e-06 Moderately Informative Direct
Cellular Component (CC) vesicle 0 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 0.1252 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 8.1e-05 Informative Direct
Cellular Component (CC) coated vesicle 0.0008409 Informative Direct
Cellular Component (CC) Golgi membrane 0.0001843 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 8.326e-12 Highly Informative Direct
Cellular Component (CC) coated pit 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.0002766 Highly Informative Direct
Cellular Component (CC) Golgi-associated vesicle 0.002606 Highly Informative Inherited
Cellular Component (CC) endocytic vesicle 0.3422 Highly Informative Inherited
Cellular Component (CC) clathrin-coated vesicle 0.8029 Highly Informative Inherited

Document: GO annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)immune system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)visual system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)lung0InformativeDirect
Xenopus ANatomical entity (XAN)spleen0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processEndocytosis0InformativeDirect
Biological processER-Golgi transport0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionLipid-binding3.01e-11InformativeDirect
Post-translational modificationAcetylation0.0007894Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009028 SSF55711 Protein matches
Abstract

The alpha and beta2 adaptor subunits can each be divided into a trunk domain and the appendage domain (or ear domain), separated by a linker region. Clathrin polymerisation is promoted by its binding to the beta2 appendage and hinge domains. The alpha appendage domain interacts with a number of accessory proteins, including eps15, epsin, amphiphysin, AP180, auxilin, numb, and Dab2, thereby regulating the translocation of these proteins to the bud site.

This entry represents a subdomain of the appendage (ear) domain of alpha- and beta-adaptin from AP clathrin adaptor complexes, and the appendage domain of the gamma subunit of coatomer complexes. These domains have a three-layer arrangement, alpha-beta-alpha, with a bifurcated antiparallel beta-sheet [PubMed10430869, PubMed10944104, [PubMed14690497]. Although the appendage domains from AP adaptins and coatomers share a similar fold, there is little sequence identity between them. However, they also share similar motif-based cargo recognition and accessory factor recruitment mechanisms.

More information about these proteins can be found at Protein of the Month: Clathrin.


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) · 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 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 Subdomain of clathrin and coatomer appendage 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 3 hidden Markov models representing the Subdomain of clathrin and coatomer appendage 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) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]